[1] "ofn"        "-oTPRAD-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/PRAD-TP/19775467/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/20064819/transformed.cor.cli.txt"

nPatients in clinical file=498, in cluster file=332, common to both=332
[1]  22 332
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            37            295 
  SPOP MUTATED SPOP WILD-TYPE 
            37            295 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            23            309 
  TP53 MUTATED TP53 WILD-TYPE 
            23            309 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             13             319 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             13             319 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             8            324 
  BRAF MUTATED BRAF WILD-TYPE 
             8            324 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             9            323 
  PTEN MUTATED PTEN WILD-TYPE 
             9            323 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           13           319 
  ATM MUTATED ATM WILD-TYPE 
           13           319 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8              324 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8              324 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
              6             326 
  MED12 MUTATED MED12 WILD-TYPE 
              6             326 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             326 
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             326 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            11            321 
  MLL2 MUTATED MLL2 WILD-TYPE 
            11            321 
[1] "AKT1 MUTATION ANALYSIS"
[1] 3
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            329 
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            329 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             4            328 
  HRAS MUTATED HRAS WILD-TYPE 
             4            328 
[1] "XPO5 MUTATION ANALYSIS"
[1] 3
  XPO5 MUTATED XPO5 WILD-TYPE 
             3            329 
  XPO5 MUTATED XPO5 WILD-TYPE 
             3            329 
[1] "KLHL2 MUTATION ANALYSIS"
[1] 3
  KLHL2 MUTATED KLHL2 WILD-TYPE 
              4             328 
  KLHL2 MUTATED KLHL2 WILD-TYPE 
              4             328 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             326 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             326 
[1] "AMFR MUTATION ANALYSIS"
[1] 3
  AMFR MUTATED AMFR WILD-TYPE 
             3            329 
  AMFR MUTATED AMFR WILD-TYPE 
             3            329 
[1] "IL6ST MUTATION ANALYSIS"
[1] 3
  IL6ST MUTATED IL6ST WILD-TYPE 
              3             329 
  IL6ST MUTATED IL6ST WILD-TYPE 
              3             329 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              6             326 
  CDK12 MUTATED CDK12 WILD-TYPE 
              6             326 
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               4              328 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               4              328 
[1] "IRF4 MUTATION ANALYSIS"
[1] 3
  IRF4 MUTATED IRF4 WILD-TYPE 
             4            328 
  IRF4 MUTATED IRF4 WILD-TYPE 
             4            328 
[1] "ASH1L MUTATION ANALYSIS"
[1] 3
  ASH1L MUTATED ASH1L WILD-TYPE 
              7             325 
  ASH1L MUTATED ASH1L WILD-TYPE 
              7             325 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            13            319 
  MLL3 MUTATED MLL3 WILD-TYPE 
            13            319 
[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] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "GLEASON_SCORE"                       
[17] "PSA_VALUE"                           
[18] "DAYS_TO_PSA"                         
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 332 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=7,	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=295,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'PSA_VALUE':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'DAYS_TO_PSA':	nDistinctValues=265,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[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] "****** SUMMARY ***** "
Output Data has 332 columns, 1 survival variables, and 10 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"    
 [4] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
 [7] "NUMBER_OF_LYMPH_NODES" "GLEASON_SCORE"         "PSA_VALUE"            
[10] "RACE"                 
YEARS_TO_BIRTH, nv=33, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
128 194   6 
[1] "table(vv)"
vv
 T2  T3  T4 
128 194   6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
128 194   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
128 194   6 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=9, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=65, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SPOP MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  SPOP MUTATED    36   1
  SPOP WILD-TYPE 287   6
  SPOP MUTATED SPOP WILD-TYPE 
            37            293 
  SPOP MUTATED SPOP WILD-TYPE 
             1              6 
$`SPOP MUTATED`
TCGA-CH-5788 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7123 
       26.99        30.31        48.13        41.85        88.34        84.56 
TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-8468 TCGA-EJ-A65E TCGA-EJ-A8FS TCGA-FC-7961 
        6.28        38.37        77.16        13.71         8.75        15.42 
TCGA-G9-6333 TCGA-G9-7510 TCGA-HC-7080 TCGA-HC-8258 TCGA-HC-8261 TCGA-J4-A6G3 
       81.04        38.96        36.36        27.85        17.95        27.91 
TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8IK 
       83.34        86.40        48.76        32.91        26.43        67.46 
TCGA-VN-A88O TCGA-VN-A88R TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87H TCGA-XJ-A83G 
       15.81        25.78       102.90        89.49        21.80        38.04 
TCGA-Y6-A8TL TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SH TCGA-YL-A8SO TCGA-ZG-A8QX 
       32.61        48.72        62.14        28.77       114.38        14.53 
TCGA-ZG-A8QY 
       13.28 

$`SPOP WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       38.50        45.73        46.92        45.40        47.90        64.60 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        58.45        60.23        60.10        49.74 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       27.09        30.35        27.68        24.39        35.28        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        38.70        36.03        28.24        36.33        36.76 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 
       45.90         3.75        42.94        32.32        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65F 
       24.85        25.18        20.58        21.96        21.96        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FU 
       15.58         6.48        15.65         4.21        10.82         4.54 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6336 
       28.41        28.83        22.36        20.25        41.62        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       55.76        49.81        67.33        50.70        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 
       45.30        39.39        44.81        64.01        40.18        38.01 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       40.31        31.50        37.97        25.15        27.29        58.22 
TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       50.73        27.91        30.97        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       19.76        65.26         4.14        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         0.72         2.10        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       24.59        26.04         1.97        17.16        30.84        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8260 
       31.43        19.36        22.42        28.27        23.87        22.55 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.78         2.01         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84       109.25        82.92        43.69        20.19        40.04 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
        6.02        25.28        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.87        10.55        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        30.71        59.67        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A6DY 
        8.65        19.66         8.88        11.57        64.70       141.21 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU 
       72.26       165.17        68.15       113.33         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       27.02        34.95        29.56        32.45        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       21.96        31.79        63.48         2.73        67.43        69.27 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-M7-A71Y 
       82.36        66.18       113.98        51.25        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       47.64        28.18        58.88        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I 
       30.38        15.58        22.55        35.44         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A872 
       25.51        24.53        25.18        41.42        44.91       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       75.91       109.58        23.93        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A9DI TCGA-XJ-A9DK 
       58.32        42.94        14.76        12.36        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
        4.80        25.32         4.87        52.96        49.02        51.45 
TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       75.75        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       45.86        46.29        32.45        77.79        68.48         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QZ 
       14.04        53.36        60.99         1.64        10.13 

  SPOP MUTATED SPOP WILD-TYPE 
          6.28           0.72 
  SPOP MUTATED SPOP WILD-TYPE 
        114.38         165.17 
  SPOP MUTATED SPOP WILD-TYPE 
         36.36          28.54 
[1] "6.3 - 114.4 (36.4)" "0.7 - 165.2 (28.5)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus              T2  T3  T4
  SPOP MUTATED    15  22   0
  SPOP WILD-TYPE 113 172   6
D1V3, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  T2           15            113
  T3           22            172
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
                cls
clus               0   1
  SPOP MUTATED    31   4
  SPOP WILD-TYPE 202  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     31    4
  SPOP WILD-TYPE  202   48
   clus
vv  SPOP MUTATED SPOP WILD-TYPE
  0           31            202
  1            4             48
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  SPOP MUTATED    29   6
  SPOP WILD-TYPE 223  30
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     29    6
  SPOP WILD-TYPE  223   30
     clus
vv    SPOP MUTATED SPOP WILD-TYPE
  NO            29            223
  YES            6             30
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus               0   1
  SPOP MUTATED     1  36
  SPOP WILD-TYPE   9 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      1   36
  SPOP WILD-TYPE    9  286
                                        clus
vv                                       SPOP MUTATED SPOP WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE              36            286
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    25   6   1   2
  SPOP WILD-TYPE 196  79   3   7
D1V7, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           25            196
  R1            6             79
  R2            1              3
  RX            2              7
[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"
D1V8, continuous
D1V9, continuous
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPOP MUTATED       0                         1    10
  SPOP WILD-TYPE     2                         6   123
D1V11, multiclass
                           clus
vv                          SPOP MUTATED SPOP WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                               10            123
[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"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    21   2
  TP53 WILD-TYPE 302   5
  TP53 MUTATED TP53 WILD-TYPE 
            23            307 
  TP53 MUTATED TP53 WILD-TYPE 
             2              5 
$`TP53 MUTATED`
TCGA-2A-A8VT TCGA-EJ-5525 TCGA-EJ-7781 TCGA-EJ-8472 TCGA-EJ-A7NH TCGA-G9-6499 
       32.71        36.66        35.28        24.85        15.58        50.73 
TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7742 TCGA-HC-8216 TCGA-HC-A48F 
       38.96        30.97        40.08         1.48        22.42        22.36 
TCGA-HI-7171 TCGA-J9-A8CK TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A7B4 TCGA-KK-A8II 
       43.69        10.55         8.65        19.66        32.45       113.98 
TCGA-VP-A876 TCGA-XJ-A9DI TCGA-YL-A8HL TCGA-YL-A8SJ TCGA-YL-A9WH 
      109.58        48.03        51.45        45.86        14.04 

$`TP53 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-CH-5737 
       20.42        43.79        22.06         3.68        25.35         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        61.87        38.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       60.10        49.74        88.34        84.56        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F 
       25.18        20.58        21.96        21.96        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        15.65         4.21        10.82         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        15.42        28.83        22.36        20.25        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       81.04        67.99        55.76        49.81        67.33        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        45.30        39.39        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       40.18        38.01        40.31        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       27.29        58.22        27.91        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         4.14        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        28.60         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 
       44.55         0.72         2.10        23.57         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       19.36        28.27        23.87        27.85        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A631 
       22.32         1.58        15.88         1.15         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        2.01         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 
      109.25        82.92        20.19        40.04         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
       27.91        16.83        22.52        10.78        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       13.87        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7FD TCGA-KC-A7FE 
       59.67        44.35        43.66        21.86         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
      165.17        68.15       113.33         6.44        58.36        27.02 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 
       34.95        29.56        74.27       101.79        21.96        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       82.36        66.18        51.25        67.46        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       47.64        28.18        58.88        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I 
       30.38        15.58        22.55        35.44         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
       25.78       119.38        75.91       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        58.32        42.94 
TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB 
       14.76        12.36        38.04         9.04         4.80        25.32 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HM TCGA-YL-A8HO 
       32.61         4.87        52.96        49.02        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       28.77        46.29        32.45       114.38        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
        8.98        53.36        60.99         1.64        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  TP53 MUTATED TP53 WILD-TYPE 
          1.48           0.72 
  TP53 MUTATED TP53 WILD-TYPE 
        113.98         165.17 
  TP53 MUTATED TP53 WILD-TYPE 
         32.71          28.70 
[1] "1.5 - 114.0 (32.7)" "0.7 - 165.2 (28.7)"
[1] "hr=" "4.5"
D2V2, continuous
                vv
clus              T2  T3  T4
  TP53 MUTATED     6  16   1
  TP53 WILD-TYPE 122 178   5
D2V3, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T2            6            122
  T3           16            178
  T4            1              5
[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"
D2V4, binary
                cls
clus               0   1
  TP53 MUTATED    16   6
  TP53 WILD-TYPE 217  46
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     16    6
  TP53 WILD-TYPE  217   46
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           16            217
  1            6             46
[1] 2 2
[1] FALSE
D2V5, binary
                cls
clus               0   1
  TP53 MUTATED    17   5
  TP53 WILD-TYPE 235  31
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     17    5
  TP53 WILD-TYPE  235   31
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            17            235
  YES            5             31
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  TP53 MUTATED     1  22
  TP53 WILD-TYPE   9 300
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   22
  TP53 WILD-TYPE    9  300
                                        clus
vv                                       TP53 MUTATED TP53 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE              22            300
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    15   8   0   0
  TP53 WILD-TYPE 206  77   4   9
D2V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           15            206
  R1            8             77
  R2            0              4
  RX            0              9
[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"
D2V8, continuous
D2V9, continuous
D2V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0     6
  TP53 WILD-TYPE     2                         7   127
D2V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                6            127
[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"

Clustering(3) Variable = FOXA1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  FOXA1 MUTATED    13   0
  FOXA1 WILD-TYPE 310   7
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             13             317 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              0               7 
$`FOXA1 MUTATED`
TCGA-CH-5737 TCGA-EJ-5494 TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-7789 TCGA-HC-7210 
        2.99        48.56         6.28        38.37        36.33        28.54 
TCGA-HC-8265 TCGA-J9-A8CP TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK 
       15.88        12.69         2.73        26.43        82.36        67.46 
TCGA-YL-A9WI 
       53.36 

$`FOXA1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 
        9.99        32.02        33.01         2.99        29.00        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        38.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       60.10        49.74        88.34        84.56        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       27.68        24.39        35.28        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.76        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       20.58        21.96        21.96        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        15.65         4.21        10.82         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 
       28.41        15.42        28.83        22.36        20.25        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       81.04        67.99        55.76        49.81        67.33        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        45.30        39.39        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       40.18        38.01        40.31        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       27.29        58.22        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
       35.44        28.18         6.08        19.76        65.26         4.14 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       36.36        37.35        14.47         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.48         1.68        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       17.16        30.84        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       28.27        23.87        27.85        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
        1.58         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84       109.25 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 
       82.92        43.69        20.19        40.04         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
       27.91        16.83        22.52        10.78        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL 
       13.87        10.55        13.32        15.22        40.67        30.71 
TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       59.67        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP 
       48.76        72.26       165.17        68.15       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.95        29.56        32.45        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
      101.79        21.96        31.79        32.91        63.48        67.43 
TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-M7-A71Y 
       69.27        66.18       113.98        51.25        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       47.64        28.18        58.88        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I 
       30.38        15.58        22.55        35.44         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       42.94        14.76        12.36        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        77.79        68.48         8.98        14.04 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         1.64        14.53        13.28        10.13 

  FOXA1 MUTATED FOXA1 WILD-TYPE 
           2.73            0.72 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
          82.36          165.17 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
          28.54           29.00 
[1] "2.7 - 82.4 (28.5)"  "0.7 - 165.2 (29.0)"
[1] "hr="     "2.6e+07"
D3V2, continuous
                 vv
clus               T2  T3  T4
  FOXA1 MUTATED     4   9   0
  FOXA1 WILD-TYPE 124 185   6
D3V3, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  T2             4             124
  T3             9             185
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
                 cls
clus                0   1
  FOXA1 MUTATED    11   1
  FOXA1 WILD-TYPE 222  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     11    1
  FOXA1 WILD-TYPE  222   51
   clus
vv  FOXA1 MUTATED FOXA1 WILD-TYPE
  0            11             222
  1             1              51
[1] 2 2
[1] FALSE
D3V5, binary
                 cls
clus                0   1
  FOXA1 MUTATED     8   1
  FOXA1 WILD-TYPE 244  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      8    1
  FOXA1 WILD-TYPE  244   35
     clus
vv    FOXA1 MUTATED FOXA1 WILD-TYPE
  NO              8             244
  YES             1              35
[1] 2 2
[1] FALSE
D3V6, binary
                 cls
clus                0   1
  FOXA1 MUTATED     0  13
  FOXA1 WILD-TYPE  10 309
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      0   13
  FOXA1 WILD-TYPE   10  309
                                        clus
vv                                       FOXA1 MUTATED FOXA1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               13             309
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXA1 MUTATED    11   2   0   0
  FOXA1 WILD-TYPE 210  83   4   9
D3V7, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  R0            11             210
  R1             2              83
  R2             0               4
  RX             0               9
[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"
D3V8, continuous
D3V9, continuous
D3V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXA1 MUTATED       0                         2     4
  FOXA1 WILD-TYPE     2                         5   129
D3V11, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               5
  WHITE                                 4             129
[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"

Clustering(4) Variable = BRAF MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     8   0
  BRAF WILD-TYPE 315   7
  BRAF MUTATED BRAF WILD-TYPE 
             8            322 
  BRAF MUTATED BRAF WILD-TYPE 
             0              7 
$`BRAF MUTATED`
TCGA-CH-5739 TCGA-EJ-5505 TCGA-EJ-7125 TCGA-EJ-A65E TCGA-HC-7742 TCGA-KC-A4BN 
       22.06        30.31        93.70        13.71         1.48        59.67 
TCGA-V1-A8MU TCGA-ZG-A8QY 
       61.68        13.28 

$`BRAF WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        2.99         6.97         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       38.50        45.73        46.92        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        38.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7314 
       60.10        49.74        88.34        84.56        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65F 
       24.85        25.18        20.58        21.96        21.96        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       15.58         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        0.72         2.10        23.57         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
        1.97        17.16        30.84        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       22.42        28.27        23.87        27.85        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.78         2.01         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84       109.25        82.92        43.69        20.19        40.04 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K 
        6.02        25.28        27.91        16.83        22.52        10.78 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
       14.37        20.28        13.87        10.55        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       40.67        12.69        30.71        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 
       86.40       141.21        48.76        72.26       165.17        68.15 
TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 
      113.33         6.44        58.36        27.02        34.95        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       32.45        74.27       101.79        21.96        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       66.18       113.98        51.25        67.46        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8WL TCGA-V1-A8WN 
       47.64        28.18        58.88        14.73        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       15.58        22.55        35.44         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53        25.18        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        58.32        42.94 
TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA 
       14.76        12.36        38.04        48.03         9.04         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       25.32        32.61         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        75.75        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        77.79        68.48         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
       60.99         1.64        14.53        10.13 

  BRAF MUTATED BRAF WILD-TYPE 
          1.48           0.72 
  BRAF MUTATED BRAF WILD-TYPE 
         93.70         165.17 
  BRAF MUTATED BRAF WILD-TYPE 
        26.185         28.915 
[1] "1.5 - 93.7 (26.2)"  "0.7 - 165.2 (28.9)"
[1] "hr="     "9300000"
D4V2, continuous
                vv
clus              T2  T3  T4
  BRAF MUTATED     3   5   0
  BRAF WILD-TYPE 125 189   6
D4V3, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T2            3            125
  T3            5            189
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
                cls
clus               0   1
  BRAF MUTATED     6   2
  BRAF WILD-TYPE 227  50
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      6    2
  BRAF WILD-TYPE  227   50
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0            6            227
  1            2             50
[1] 2 2
[1] FALSE
D4V5, binary
                cls
clus               0   1
  BRAF MUTATED     7   0
  BRAF WILD-TYPE 245  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      7    0
  BRAF WILD-TYPE  245   36
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  NO             7            245
  YES            0             36
[1] 2 2
[1] FALSE
D4V6, binary
                cls
clus               0   1
  BRAF MUTATED     1   7
  BRAF WILD-TYPE   9 315
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1    7
  BRAF WILD-TYPE    9  315
                                        clus
vv                                       BRAF MUTATED BRAF WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE               7            315
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED     6   1   0   1
  BRAF WILD-TYPE 215  84   4   8
D4V7, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0            6            215
  R1            1             84
  R2            0              4
  RX            1              8
[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"
D4V8, continuous
D4V9, continuous
D4V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       0                         0     4
  BRAF WILD-TYPE     2                         7   129
D4V11, multiclass
                           clus
vv                          BRAF MUTATED BRAF WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                4            129
[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"

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  PTEN MUTATED     9   0
  PTEN WILD-TYPE 314   7
  PTEN MUTATED PTEN WILD-TYPE 
             9            321 
  PTEN MUTATED PTEN WILD-TYPE 
             0              7 
$`PTEN MUTATED`
TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5791 TCGA-EJ-7791 TCGA-FC-7961 TCGA-HC-7212 
        2.99         1.02        33.01        36.76        15.42        28.60 
TCGA-HC-7230 TCGA-KC-A4BV TCGA-KK-A8I6 
        1.68        43.66        21.96 

$`PTEN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        6.97        22.06        12.99         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        58.45        60.23        41.85        60.10 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       49.74        88.34        84.56        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       38.70        36.03        28.24        36.33        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F 
       25.18        20.58        21.96        21.96        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       15.58         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 
        4.54        28.41        28.83        22.36        20.25        41.62 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       81.04        67.99        55.76        49.81        67.33        50.70 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        45.30        39.39        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       40.18        38.01        40.31        31.50        37.97        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       27.29        58.22        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
       35.44        28.18         6.08        19.76        65.26         4.14 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 
       36.36        37.35        14.47        28.54         0.79        40.08 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 
        2.37        38.17        44.55         0.72         2.10        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97        17.16 
TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       23.87        27.85        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84       109.25 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 
       82.92        43.69        20.19        40.04         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
       27.91        16.83        22.52        10.78        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.87        10.55        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       30.71        59.67        44.35        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP 
       48.76        72.26       165.17        68.15       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.95        29.56        32.45        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
      101.79        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 
       67.46        20.65         5.19        12.62        13.15        18.84 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12         0.89        47.64        28.18        58.88 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       35.44         6.64         8.84        25.51        24.53        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR 
       66.97        21.80        58.32        42.94        14.76        12.36 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       38.04        48.03         9.04         4.80        25.32        32.61 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW 
       68.48         8.98        14.04        53.36        60.99         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  PTEN MUTATED PTEN WILD-TYPE 
          1.02           0.72 
  PTEN MUTATED PTEN WILD-TYPE 
         43.66         165.17 
  PTEN MUTATED PTEN WILD-TYPE 
         21.96          29.56 
[1] "1.0 - 43.7 (22.0)"  "0.7 - 165.2 (29.6)"
[1] "hr="     "9200000"
D5V2, continuous
                vv
clus              T2  T3  T4
  PTEN MUTATED     5   4   0
  PTEN WILD-TYPE 123 190   6
D5V3, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T2            5            123
  T3            4            190
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
                cls
clus               0   1
  PTEN MUTATED     9   0
  PTEN WILD-TYPE 224  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      9    0
  PTEN WILD-TYPE  224   52
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            9            224
  1            0             52
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus               0   1
  PTEN MUTATED     5   0
  PTEN WILD-TYPE 247  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE  247   36
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO             5            247
  YES            0             36
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus               0   1
  PTEN MUTATED     0   9
  PTEN WILD-TYPE  10 313
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0    9
  PTEN WILD-TYPE   10  313
                                        clus
vv                                       PTEN MUTATED PTEN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               9            313
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     6   1   0   0
  PTEN WILD-TYPE 215  84   4   9
D5V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            6            215
  R1            1             84
  R2            0              4
  RX            0              9
[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"
D5V8, continuous
D5V9, continuous
D5V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0     7
  PTEN WILD-TYPE     2                         7   126
D5V11, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                7            126
[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"

Clustering(6) Variable = ATM MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  ATM MUTATED    12   1
  ATM WILD-TYPE 311   6
  ATM MUTATED ATM WILD-TYPE 
           13           317 
  ATM MUTATED ATM WILD-TYPE 
            1             6 
$`ATM MUTATED`
TCGA-CH-5762 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7783 TCGA-EJ-7784 
       44.02        47.90        48.53        69.63        25.87        25.68 
TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-A4ZV TCGA-M7-A725 TCGA-YL-A8S9 TCGA-YL-A8SC 
       38.96        30.97         0.76        18.84        60.56        41.46 
TCGA-YL-A8SH 
       28.77 

$`ATM WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04         0.92        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
       38.50        45.73        46.92        30.31        45.40        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       48.13        62.04        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       62.10        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        58.45        60.23        41.85        60.10        49.74 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       88.34        84.56        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       24.39        35.28        38.37        38.70        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       36.33        36.76        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        21.96        13.71        18.41        21.90        14.83 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 
       15.65         4.21        10.82         8.75         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 
       15.42        28.83        22.36        20.25        41.62        81.04 
TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       67.99        55.76        49.81        67.33        50.70        47.15 
TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        45.30        39.39        44.81        64.01        40.18 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       38.01        40.31        31.50        37.97        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       58.22        50.73        27.91        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         4.14        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         0.72         2.10        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 
        1.68        24.59        26.04         1.97        17.16        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       27.85        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X 
        1.15        22.36         1.78         2.01         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84       109.25        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       20.19        40.04         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK 
       22.52        10.78        14.37        20.28        13.87        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU 
       72.26       165.17        68.15       113.33         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       27.02        34.95        29.56        32.45        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-QU-A6IP 
       67.46        20.65         5.19        12.62        13.15        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML 
       18.12         0.89        47.64        28.18        58.88        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        25.51        24.53        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       16.83        56.52        45.14        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        77.79        68.48         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         1.64        14.53        13.28        10.13 

  ATM MUTATED ATM WILD-TYPE 
         0.76          0.72 
  ATM MUTATED ATM WILD-TYPE 
        69.63        165.17 
  ATM MUTATED ATM WILD-TYPE 
        38.96         28.70 
[1] "0.8 - 69.6 (39.0)"  "0.7 - 165.2 (28.7)"
[1] "hr=" "4.4"
D6V2, continuous
               vv
clus             T2  T3  T4
  ATM MUTATED     1  11   1
  ATM WILD-TYPE 127 183   5
D6V3, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T2           1           127
  T3          11           183
  T4           1             5
[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"
D6V4, binary
               cls
clus              0   1
  ATM MUTATED    11   2
  ATM WILD-TYPE 222  50
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     11    2
  ATM WILD-TYPE  222   50
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          11           222
  1           2            50
[1] 2 2
[1] FALSE
D6V5, binary
               cls
clus              0   1
  ATM MUTATED    11   1
  ATM WILD-TYPE 241  35
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     11    1
  ATM WILD-TYPE  241   35
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           11           241
  YES           1            35
[1] 2 2
[1] FALSE
D6V6, binary
               cls
clus              0   1
  ATM MUTATED     0  13
  ATM WILD-TYPE  10 309
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      0   13
  ATM WILD-TYPE   10  309
                                        clus
vv                                       ATM MUTATED ATM WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE           0            10
  PROSTATE ADENOCARCINOMA ACINAR TYPE             13           309
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED     6   7   0   0
  ATM WILD-TYPE 215  78   4   9
D6V7, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0           6           215
  R1           7            78
  R2           0             4
  RX           0             9
[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"
D6V8, continuous
D6V9, continuous
D6V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         1     5
  ATM WILD-TYPE     2                         6   128
D6V11, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             6
  WHITE                               5           128
[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"

Clustering(7) Variable = CTNNB1 MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED     8   0
  CTNNB1 WILD-TYPE 315   7
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               8              322 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               0                7 
$`CTNNB1 MUTATED`
TCGA-CH-5739 TCGA-CH-5752 TCGA-EJ-5494 TCGA-EJ-5525 TCGA-HC-7212 TCGA-HC-8262 
       22.06        31.00        48.56        36.66        28.60        22.32 
TCGA-KK-A6DY TCGA-VP-A87H 
      141.21        21.80 

$`CTNNB1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        2.99         6.97         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        35.01         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
       32.02        33.01         2.99        29.00        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        58.45        60.23        41.85        60.10        49.74 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       88.34        84.56        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       36.03        28.24        36.33        36.76        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F 
       25.18        20.58        21.96        21.96        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       15.58         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        2.10        23.57         1.48         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
        1.97        17.16        30.84        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       22.42        28.27        23.87        27.85        22.55        17.95 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        2.01         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T 
      109.25        82.92        43.69        20.19        40.04         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
       25.28        27.91        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.87        10.55        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        30.71        59.67        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 
       86.40        48.76        72.26       165.17        68.15       113.33 
TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 
        6.44        58.36        27.02        34.95        29.56        32.45 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       74.27       101.79        21.96        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 
      113.98        51.25        67.46        20.65         5.19        12.62 
TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF 
       13.15        18.84        86.14        18.12         0.89        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       28.18        58.88        14.73        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       15.58        22.55        35.44         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53        25.18        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        60.92        66.97        58.32        42.94        14.76 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB 
       12.36        38.04        48.03         9.04         4.80        25.32 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       75.75        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       77.79        68.48         8.98        14.04        53.36        60.99 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.64        14.53        13.28        10.13 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           21.80             0.72 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          141.21           165.17 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          29.800           28.915 
[1] "21.8 - 141.2 (29.8)" "0.7 - 165.2 (28.9)" 
[1] "hr="   "3e+07"
D7V2, continuous
                  vv
clus                T2  T3  T4
  CTNNB1 MUTATED     4   4   0
  CTNNB1 WILD-TYPE 124 190   6
D7V3, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T2              4              124
  T3              4              190
  T4              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     8   0
  CTNNB1 WILD-TYPE 225  52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      8    0
  CTNNB1 WILD-TYPE  225   52
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0              8              225
  1              0               52
[1] 2 2
[1] FALSE
D7V5, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     6   1
  CTNNB1 WILD-TYPE 246  35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6    1
  CTNNB1 WILD-TYPE  246   35
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO               6              246
  YES              1               35
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     0   8
  CTNNB1 WILD-TYPE  10 314
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      0    8
  CTNNB1 WILD-TYPE   10  314
                                        clus
vv                                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 8              314
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED     5   1   1   0
  CTNNB1 WILD-TYPE 216  84   3   9
D7V7, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              5              216
  R1              1               84
  R2              1                3
  RX              0                9
[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"
D7V8, continuous
D7V9, continuous
D7V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED       0                         0     5
  CTNNB1 WILD-TYPE     2                         7   128
D7V11, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              128
[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"

Clustering(8) Variable = MED12 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  MED12 MUTATED     6   0
  MED12 WILD-TYPE 317   7
  MED12 MUTATED MED12 WILD-TYPE 
              6             324 
  MED12 MUTATED MED12 WILD-TYPE 
              0               7 
$`MED12 MUTATED`
TCGA-CH-5748 TCGA-EJ-5510 TCGA-EJ-7792 TCGA-G9-7519 TCGA-KC-A7F3 TCGA-VP-A87J 
        1.02        62.04        45.90        27.91        21.86        58.32 

$`MED12 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       64.60        48.13        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       62.10        62.10        69.63        64.50        74.93        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       61.87        36.66        38.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       60.10        49.74        88.34        84.56        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        38.70        36.03        28.24        36.33        36.76 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        28.83        22.36 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 
       20.25        41.62        81.04        67.99        55.76        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       67.33        50.70        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       44.81        64.01        40.18        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 
       37.97        25.15        27.29        58.22        50.73        38.96 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
       19.36        22.42        28.27        23.87        27.85        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        0.76         1.78         2.01         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A4BV TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
       43.66         8.65        19.66         8.88        11.57        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 
       68.15       113.33         6.44        58.36        27.02        34.95 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 
       29.56        32.45        74.27       101.79        21.96        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        67.46        20.65 
TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 
        5.19        12.62        13.15        18.84        86.14        18.12 
TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU 
        0.89        47.64        28.18        58.88        14.73        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51        24.53        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        55.56        60.92        66.97        21.80 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       42.94        14.76        12.36        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        77.79        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       53.36        60.99         1.64        14.53        13.28        10.13 

  MED12 MUTATED MED12 WILD-TYPE 
           1.02            0.72 
  MED12 MUTATED MED12 WILD-TYPE 
          62.04          165.17 
  MED12 MUTATED MED12 WILD-TYPE 
         36.905          28.915 
[1] "1.0 - 62.0 (36.9)"  "0.7 - 165.2 (28.9)"
[1] "hr="     "9200000"
D8V2, continuous
                 vv
clus               T2  T3  T4
  MED12 MUTATED     4   2   0
  MED12 WILD-TYPE 124 192   6
D8V3, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  T2             4             124
  T3             2             192
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
                 cls
clus                0   1
  MED12 MUTATED     4   1
  MED12 WILD-TYPE 229  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      4    1
  MED12 WILD-TYPE  229   51
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             4             229
  1             1              51
[1] 2 2
[1] FALSE
D8V5, binary
                 cls
clus                0   1
  MED12 MUTATED     5   0
  MED12 WILD-TYPE 247  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      5    0
  MED12 WILD-TYPE  247   36
     clus
vv    MED12 MUTATED MED12 WILD-TYPE
  NO              5             247
  YES             0              36
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus                0   1
  MED12 MUTATED     0   6
  MED12 WILD-TYPE  10 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      0    6
  MED12 WILD-TYPE   10  316
                                        clus
vv                                       MED12 MUTATED MED12 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             316
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED12 MUTATED     4   1   1   0
  MED12 WILD-TYPE 217  84   3   9
D8V7, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0             4             217
  R1             1              84
  R2             1               3
  RX             0               9
[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"
D8V8, continuous
D8V9, continuous
D8V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED       0                         0     3
  MED12 WILD-TYPE     2                         7   130
D8V11, multiclass
                           clus
vv                          MED12 MUTATED MED12 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             130
[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"

Clustering(9) Variable = KDM6A MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     6   0
  KDM6A WILD-TYPE 317   7
  KDM6A MUTATED KDM6A WILD-TYPE 
              6             324 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0               7 
$`KDM6A MUTATED`
TCGA-EJ-5509 TCGA-EJ-7317 TCGA-EJ-7331 TCGA-HC-7212 TCGA-V1-A8ML TCGA-XA-A8JR 
       48.13        25.35        24.39        28.60        14.73        12.36 

$`KDM6A WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       47.90        64.60        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        38.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        60.10        49.74        88.34        84.56        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       83.57        37.81        33.14        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        28.83        22.36 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 
       20.25        41.62        81.04        67.99        55.76        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       67.33        50.70        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       44.81        64.01        40.18        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 
       37.97        25.15        27.29        58.22        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 
       27.91        30.97        35.44        28.18         6.08        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         4.14        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
        0.79        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
       19.36        22.42        28.27        23.87        27.85        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        0.76         1.78         2.01         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
      165.17        68.15       113.33         6.44        58.36        27.02 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        29.56        32.45        74.27       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP 
       20.65         5.19        12.62        13.15        18.84        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MU 
       18.12         0.89        47.64        28.18        58.88        61.68 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 
       64.04        30.38        15.58        22.55        35.44         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51        24.53        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        89.49        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       58.32        42.94        14.76        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        77.79        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       53.36        60.99         1.64        14.53        13.28        10.13 

  KDM6A MUTATED KDM6A WILD-TYPE 
          12.36            0.72 
  KDM6A MUTATED KDM6A WILD-TYPE 
          48.13          165.17 
  KDM6A MUTATED KDM6A WILD-TYPE 
         24.870          29.935 
[1] "12.4 - 48.1 (24.9)" "0.7 - 165.2 (29.9)"
[1] "hr="     "9100000"
D9V2, continuous
                 vv
clus               T2  T3  T4
  KDM6A MUTATED     6   0   0
  KDM6A WILD-TYPE 122 194   6
D9V3, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T2             6             122
  T3             0             194
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
                 cls
clus                0   1
  KDM6A MUTATED     6   0
  KDM6A WILD-TYPE 227  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      6    0
  KDM6A WILD-TYPE  227   52
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             6             227
  1             0              52
[1] 2 2
[1] FALSE
D9V5, binary
                 cls
clus                0   1
  KDM6A MUTATED     5   0
  KDM6A WILD-TYPE 247  36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      5    0
  KDM6A WILD-TYPE  247   36
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO              5             247
  YES             0              36
[1] 2 2
[1] FALSE
D9V6, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   6
  KDM6A WILD-TYPE  10 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    6
  KDM6A WILD-TYPE   10  316
                                        clus
vv                                       KDM6A MUTATED KDM6A WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             316
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED     4   0   1   0
  KDM6A WILD-TYPE 217  85   3   9
D9V7, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0             4             217
  R1             0              85
  R2             1               3
  RX             0               9
[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"
D9V8, continuous
D9V9, continuous
D9V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       0                         0     4
  KDM6A WILD-TYPE     2                         7   129
D9V11, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             129
[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"

Clustering(10) Variable = MLL2 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    11   0
  MLL2 WILD-TYPE 312   7
  MLL2 MUTATED MLL2 WILD-TYPE 
            11            319 
  MLL2 MUTATED MLL2 WILD-TYPE 
             0              7 
$`MLL2 MUTATED`
TCGA-EJ-5495 TCGA-EJ-5531 TCGA-EJ-8468 TCGA-EJ-A8FN TCGA-HC-8216 TCGA-HI-7170 
       57.86        41.85        77.16        10.82        22.42        82.92 
TCGA-KC-A7FA TCGA-KK-A6E5 TCGA-KK-A7AP TCGA-VN-A88P TCGA-YL-A8SB 
       19.66        68.15         6.44        41.42        56.52 

$`MLL2 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       48.56        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        38.76        58.45        60.23 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       60.10        49.74        88.34        84.56        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        35.28        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        38.70        36.03        28.24        36.33        36.76 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 
       45.90         3.75        42.94        32.32        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FS 
       14.20        15.58         6.48        15.65         4.21         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       19.36        28.27        23.87        27.85        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.78         2.01         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T 
       18.84       109.25        43.69        20.19        40.04         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
       25.28        27.91        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.87        10.55        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        30.71        59.67        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.65         8.88        11.57        83.34        64.70        86.40 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E6 TCGA-KK-A7AU 
      141.21        48.76        72.26       165.17       113.33        58.36 
TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       27.02        34.95        29.56        32.45        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 
       67.46        20.65         5.19        12.62        13.15        18.84 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12         0.89        47.64        28.18        58.88 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       35.44         6.64         8.84        25.51        24.53        25.18 
TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       15.81        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       60.56        16.83        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        77.79        68.48         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       14.04        53.36        60.99         1.64        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  MLL2 MUTATED MLL2 WILD-TYPE 
          6.44           0.72 
  MLL2 MUTATED MLL2 WILD-TYPE 
         82.92         165.17 
  MLL2 MUTATED MLL2 WILD-TYPE 
         41.85          28.77 
[1] "6.4 - 82.9 (41.9)"  "0.7 - 165.2 (28.8)"
[1] "hr="     "2.6e+07"
D10V2, continuous
                vv
clus              T2  T3  T4
  MLL2 MUTATED     3   8   0
  MLL2 WILD-TYPE 125 186   6
D10V3, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T2            3            125
  T3            8            186
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
                cls
clus               0   1
  MLL2 MUTATED     9   2
  MLL2 WILD-TYPE 224  50
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      9    2
  MLL2 WILD-TYPE  224   50
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0            9            224
  1            2             50
[1] 2 2
[1] FALSE
D10V5, binary
                cls
clus               0   1
  MLL2 MUTATED     9   1
  MLL2 WILD-TYPE 243  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      9    1
  MLL2 WILD-TYPE  243   35
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO             9            243
  YES            1             35
[1] 2 2
[1] FALSE
D10V6, binary
                cls
clus               0   1
  MLL2 MUTATED     0  11
  MLL2 WILD-TYPE  10 311
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      0   11
  MLL2 WILD-TYPE   10  311
                                        clus
vv                                       MLL2 MUTATED MLL2 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE              11            311
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED     9   2   0   0
  MLL2 WILD-TYPE 212  83   4   9
D10V7, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0            9            212
  R1            2             83
  R2            0              4
  RX            0              9
[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"
D10V8, continuous
D10V9, continuous
D10V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       0                         0     3
  MLL2 WILD-TYPE     2                         7   130
D10V11, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            130
[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"

Clustering(11) Variable = AKT1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  AKT1 MUTATED     3   0
  AKT1 WILD-TYPE 320   7
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            327 
  AKT1 MUTATED AKT1 WILD-TYPE 
             0              7 
$`AKT1 MUTATED`
TCGA-EJ-5530 TCGA-J4-A83M TCGA-V1-A8WW 
       60.23        14.37        35.44 

$`AKT1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        38.76        58.45 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        60.10        49.74        88.34        84.56        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.76        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G 
       76.41        38.10        24.85        25.18        20.58        21.96 
TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       21.96        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       55.76        49.81        67.33        50.70        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 
       45.30        39.39        44.81        64.01        40.18        38.01 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       40.31        31.50        37.97        25.15        27.29        58.22 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.44        28.18 
TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        6.08        19.76        65.26         4.14        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 
        2.37        38.17        44.55         0.72         2.10        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97        17.16 
TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       23.87        27.85        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84       109.25 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 
       82.92        43.69        20.19        40.04         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83N TCGA-J9-A52B 
       27.91        16.83        22.52        10.78        20.28        13.87 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.55        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       59.67        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP 
       48.76        72.26       165.17        68.15       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.95        29.56        32.45        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
      101.79        21.96        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 
       51.25        67.46        20.65         5.19        12.62        13.15 
TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG 
       18.84        86.14        18.12         0.89        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       58.88        14.73        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       22.55         6.64         8.84        25.51        24.53        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR 
       66.97        21.80        58.32        42.94        14.76        12.36 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       38.04        48.03         9.04         4.80        25.32        32.61 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW 
       68.48         8.98        14.04        53.36        60.99         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  AKT1 MUTATED AKT1 WILD-TYPE 
         14.37           0.72 
  AKT1 MUTATED AKT1 WILD-TYPE 
         60.23         165.17 
  AKT1 MUTATED AKT1 WILD-TYPE 
         35.44          28.83 
[1] "14.4 - 60.2 (35.4)" "0.7 - 165.2 (28.8)"
[1] "hr="     "3300000"
D11V2, continuous
                vv
clus              T2  T3  T4
  AKT1 MUTATED     2   1   0
  AKT1 WILD-TYPE 126 193   6
D11V3, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  T2            2            126
  T3            1            193
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V4, binary
                cls
clus               0   1
  AKT1 MUTATED     2   1
  AKT1 WILD-TYPE 231  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      2    1
  AKT1 WILD-TYPE  231   51
   clus
vv  AKT1 MUTATED AKT1 WILD-TYPE
  0            2            231
  1            1             51
[1] 2 2
[1] FALSE
D11V5, binary
                cls
clus               0   1
  AKT1 MUTATED     3   0
  AKT1 WILD-TYPE 249  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      3    0
  AKT1 WILD-TYPE  249   36
     clus
vv    AKT1 MUTATED AKT1 WILD-TYPE
  NO             3            249
  YES            0             36
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus               0   1
  AKT1 MUTATED     0   3
  AKT1 WILD-TYPE  10 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      0    3
  AKT1 WILD-TYPE   10  319
                                        clus
vv                                       AKT1 MUTATED AKT1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            319
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AKT1 MUTATED     2   1   0   0
  AKT1 WILD-TYPE 219  84   4   9
D11V7, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  R0            2            219
  R1            1             84
  R2            0              4
  RX            0              9
[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"
D11V8, continuous
D11V9, continuous
D11V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKT1 MUTATED       0                         0     1
  AKT1 WILD-TYPE     2                         7   132
D11V11, multiclass
[1] "Remove cluster labels:" "AKT1 MUTATED"          
clus
  AKT1 MUTATED AKT1 WILD-TYPE 
             1            141 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5744     TCGA-CH-5746     TCGA-CH-5748 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5531 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6329     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6342 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370     TCGA-G9-6371 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7747 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7818 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7170 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HI-7171 
"AKT1 WILD-TYPE" 

Clustering(12) Variable = HRAS MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     4   0
  HRAS WILD-TYPE 319   7
  HRAS MUTATED HRAS WILD-TYPE 
             4            326 
  HRAS MUTATED HRAS WILD-TYPE 
             0              7 
$`HRAS MUTATED`
TCGA-EJ-A7NJ TCGA-G9-6361 TCGA-HI-7168 TCGA-VN-A88N 
        6.48        46.52       109.25        25.18 

$`HRAS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        38.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        60.10        49.74        88.34        84.56 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        30.35        27.68         6.28        24.39        35.28 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        38.70        36.03        28.24 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       36.33        36.76        45.90         3.75        42.94        32.32 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       77.16        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        21.96        13.71        18.41        21.90        14.83 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20        15.58        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6363 
       55.76        49.81        67.33        50.70        47.15        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81        64.01        40.18        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 
       31.50        37.97        25.15        27.29        58.22        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       38.96        27.91        30.97        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         4.14        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         0.72         2.10        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 
        1.68        24.59        26.04         1.97        17.16        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       27.85        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W 
        1.15        22.36         0.76         1.78         2.01         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7170 TCGA-HI-7171 
        4.93         9.53        25.48        18.84        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       20.19        40.04         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK 
       22.52        10.78        14.37        20.28        13.87        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 
       11.57        83.34        64.70        86.40       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU 
       72.26       165.17        68.15       113.33         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       27.02        34.95        29.56        32.45        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 
       67.46        20.65         5.19        12.62        13.15        18.84 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12         0.89        47.64        28.18        58.88 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88O 
       35.44         6.64         8.84        25.51        24.53        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
        8.98        14.04        53.36        60.99         1.64        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  HRAS MUTATED HRAS WILD-TYPE 
          6.48           0.72 
  HRAS MUTATED HRAS WILD-TYPE 
        109.25         165.17 
  HRAS MUTATED HRAS WILD-TYPE 
        35.850         28.915 
[1] "6.5 - 109.2 (35.9)" "0.7 - 165.2 (28.9)"
[1] "hr="     "9100000"
D12V2, continuous
                vv
clus              T2  T3  T4
  HRAS MUTATED     2   2   0
  HRAS WILD-TYPE 126 192   6
D12V3, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T2            2            126
  T3            2            192
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V4, binary
                cls
clus               0   1
  HRAS MUTATED     4   0
  HRAS WILD-TYPE 229  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      4    0
  HRAS WILD-TYPE  229   52
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            4            229
  1            0             52
[1] 2 2
[1] FALSE
D12V5, binary
                cls
clus               0   1
  HRAS MUTATED     4   0
  HRAS WILD-TYPE 248  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      4    0
  HRAS WILD-TYPE  248   36
     clus
vv    HRAS MUTATED HRAS WILD-TYPE
  NO             4            248
  YES            0             36
[1] 2 2
[1] FALSE
D12V6, binary
                cls
clus               0   1
  HRAS MUTATED     0   4
  HRAS WILD-TYPE  10 318
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0    4
  HRAS WILD-TYPE   10  318
                                        clus
vv                                       HRAS MUTATED HRAS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            318
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HRAS MUTATED     3   1   0   0
  HRAS WILD-TYPE 218  84   4   9
D12V7, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            3            218
  R1            1             84
  R2            0              4
  RX            0              9
[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"
D12V8, continuous
D12V9, continuous
D12V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       0                         0     2
  HRAS WILD-TYPE     2                         7   131
D12V11, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2            140 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5744     TCGA-CH-5746     TCGA-CH-5748 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6333     TCGA-G9-6336 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370     TCGA-G9-6371 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7747 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7818 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7170     TCGA-HI-7171 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 

Clustering(13) Variable = XPO5 MUTATION ANALYSIS
D13V1, survival
                sevent
clus2              0   1
  XPO5 MUTATED     3   0
  XPO5 WILD-TYPE 320   7
  XPO5 MUTATED XPO5 WILD-TYPE 
             3            327 
  XPO5 MUTATED XPO5 WILD-TYPE 
             0              7 
$`XPO5 MUTATED`
TCGA-CH-5739 TCGA-G9-6377 TCGA-KK-A6E6 
       22.06        31.50       113.33 

$`XPO5 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        2.99         6.97         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        38.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        60.10        49.74        88.34        84.56        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.76        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G 
       76.41        38.10        24.85        25.18        20.58        21.96 
TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       21.96        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       55.76        49.81        67.33        50.70        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 
       45.30        39.39        44.81        64.01        40.18        38.01 
TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 
       40.31        37.97        25.15        27.29        58.22        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       38.96        27.91        30.97        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         4.14        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         0.72         2.10        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 
        1.68        24.59        26.04         1.97        17.16        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       27.85        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W 
        1.15        22.36         0.76         1.78         2.01         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 
        4.93         9.53        25.48        18.84       109.25        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       43.69        20.19        40.04         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       16.83        22.52        10.78        14.37        20.28        13.87 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.55        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       59.67        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A7AP TCGA-KK-A7AU 
       48.76        72.26       165.17        68.15         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       27.02        34.95        29.56        32.45        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       21.96        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 
       67.46        20.65         5.19        12.62        13.15        18.84 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       86.14        18.12         0.89        47.64        28.18        58.88 
TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N 
       35.44         6.64         8.84        25.51        24.53        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       119.38        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58       102.90        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR 
       66.97        21.80        58.32        42.94        14.76        12.36 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       38.04        48.03         9.04         4.80        25.32        32.61 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW 
       68.48         8.98        14.04        53.36        60.99         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  XPO5 MUTATED XPO5 WILD-TYPE 
         22.06           0.72 
  XPO5 MUTATED XPO5 WILD-TYPE 
        113.33         165.17 
  XPO5 MUTATED XPO5 WILD-TYPE 
         31.50          28.83 
[1] "22.1 - 113.3 (31.5)" "0.7 - 165.2 (28.8)" 
[1] "hr="     "9100000"
D13V2, continuous
                vv
clus              T2  T3  T4
  XPO5 MUTATED     1   2   0
  XPO5 WILD-TYPE 127 192   6
D13V3, multiclass
    clus
vv   XPO5 MUTATED XPO5 WILD-TYPE
  T2            1            127
  T3            2            192
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V4, binary
                cls
clus               0   1
  XPO5 MUTATED     3   0
  XPO5 WILD-TYPE 230  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO5 MUTATED      3    0
  XPO5 WILD-TYPE  230   52
   clus
vv  XPO5 MUTATED XPO5 WILD-TYPE
  0            3            230
  1            0             52
[1] 2 2
[1] FALSE
D13V5, binary
                cls
clus               0   1
  XPO5 MUTATED     3   0
  XPO5 WILD-TYPE 249  36
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO5 MUTATED      3    0
  XPO5 WILD-TYPE  249   36
     clus
vv    XPO5 MUTATED XPO5 WILD-TYPE
  NO             3            249
  YES            0             36
[1] 2 2
[1] FALSE
D13V6, binary
                cls
clus               0   1
  XPO5 MUTATED     0   3
  XPO5 WILD-TYPE  10 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  XPO5 MUTATED      0    3
  XPO5 WILD-TYPE   10  319
                                        clus
vv                                       XPO5 MUTATED XPO5 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            319
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  XPO5 MUTATED     3   0   0   0
  XPO5 WILD-TYPE 218  85   4   9
D13V7, multiclass
    clus
vv   XPO5 MUTATED XPO5 WILD-TYPE
  R0            3            218
  R1            0             85
  R2            0              4
  RX            0              9
[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"
D13V8, continuous
D13V9, continuous
D13V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XPO5 MUTATED       0                         0     2
  XPO5 WILD-TYPE     2                         7   131
D13V11, multiclass
[1] "Remove cluster labels:" "XPO5 MUTATED"          
clus
  XPO5 MUTATED XPO5 WILD-TYPE 
             2            140 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5740     TCGA-CH-5741 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5744     TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6329     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6342 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370     TCGA-G9-6371 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075     TCGA-HC-7077 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7081 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231     TCGA-HC-7232 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7747     TCGA-HC-7748 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7818     TCGA-HC-7820 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 
    TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7170     TCGA-HI-7171 
"XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" "XPO5 WILD-TYPE" 

Clustering(14) Variable = KLHL2 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  KLHL2 MUTATED     4   0
  KLHL2 WILD-TYPE 319   7
  KLHL2 MUTATED KLHL2 WILD-TYPE 
              4             326 
  KLHL2 MUTATED KLHL2 WILD-TYPE 
              0               7 
$`KLHL2 MUTATED`
TCGA-CH-5737 TCGA-EJ-5527 TCGA-EJ-7115 TCGA-EJ-A65F 
        2.99        58.45        88.34        18.41 

$`KLHL2 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        6.97        22.06         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        61.87        36.66        38.76        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       60.10        49.74        84.56        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       15.58         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
       19.36        22.42        28.27        23.87        27.85        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        0.76         1.78         2.01         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
      165.17        68.15       113.33         6.44        58.36        27.02 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        29.56        32.45        74.27       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP 
       20.65         5.19        12.62        13.15        18.84        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML 
       18.12         0.89        47.64        28.18        58.88        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        25.51        24.53        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
        8.98        14.04        53.36        60.99         1.64        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  KLHL2 MUTATED KLHL2 WILD-TYPE 
           2.99            0.72 
  KLHL2 MUTATED KLHL2 WILD-TYPE 
          88.34          165.17 
  KLHL2 MUTATED KLHL2 WILD-TYPE 
         38.430          28.915 
[1] "3.0 - 88.3 (38.4)"  "0.7 - 165.2 (28.9)"
[1] "hr="     "9100000"
D14V2, continuous
                 vv
clus               T2  T3  T4
  KLHL2 MUTATED     1   3   0
  KLHL2 WILD-TYPE 127 191   6
D14V3, multiclass
    clus
vv   KLHL2 MUTATED KLHL2 WILD-TYPE
  T2             1             127
  T3             3             191
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V4, binary
                 cls
clus                0   1
  KLHL2 MUTATED     4   0
  KLHL2 WILD-TYPE 229  52
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL2 MUTATED      4    0
  KLHL2 WILD-TYPE  229   52
   clus
vv  KLHL2 MUTATED KLHL2 WILD-TYPE
  0             4             229
  1             0              52
[1] 2 2
[1] FALSE
D14V5, binary
                 cls
clus                0   1
  KLHL2 MUTATED     2   1
  KLHL2 WILD-TYPE 250  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL2 MUTATED      2    1
  KLHL2 WILD-TYPE  250   35
     clus
vv    KLHL2 MUTATED KLHL2 WILD-TYPE
  NO              2             250
  YES             1              35
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus                0   1
  KLHL2 MUTATED     1   3
  KLHL2 WILD-TYPE   9 319
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KLHL2 MUTATED      1    3
  KLHL2 WILD-TYPE    9  319
                                        clus
vv                                       KLHL2 MUTATED KLHL2 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1               9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             319
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KLHL2 MUTATED     4   0   0   0
  KLHL2 WILD-TYPE 217  85   4   9
D14V7, multiclass
    clus
vv   KLHL2 MUTATED KLHL2 WILD-TYPE
  R0             4             217
  R1             0              85
  R2             0               4
  RX             0               9
[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"
D14V8, continuous
D14V9, continuous
D14V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLHL2 MUTATED       0                         0     3
  KLHL2 WILD-TYPE     2                         7   130
D14V11, multiclass
                           clus
vv                          KLHL2 MUTATED KLHL2 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             130
[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"

Clustering(15) Variable = ZMYM3 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  ZMYM3 MUTATED     6   0
  ZMYM3 WILD-TYPE 317   7
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              6             324 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              0               7 
$`ZMYM3 MUTATED`
TCGA-CH-5738 TCGA-CH-5741 TCGA-CH-5772 TCGA-HC-A76W TCGA-KC-A4BV TCGA-KK-A7AP 
        6.97        12.99        15.98         7.00        43.66         6.44 

$`ZMYM3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 
        2.99        22.06         1.02         1.97        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
       13.02        35.01        31.00         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        13.02        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        48.56        57.86        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        56.55        46.52        44.88        38.50        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       46.92        30.31        45.40        47.90        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       62.04        48.53        56.98        60.13        60.23        62.10 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        58.45        60.23        41.85        60.10 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       49.74        88.34        84.56        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        28.83        22.36 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 
       20.25        41.62        81.04        67.99        55.76        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       67.33        50.70        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       44.81        64.01        40.18        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 
       37.97        25.15        27.29        58.22        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 
       27.91        30.97        35.44        28.18         6.08        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         4.14        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         0.72         2.10        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       24.59        26.04         1.97        17.16        30.84        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76X TCGA-HC-A8CY 
       22.36         0.76         1.78         2.01         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
       21.86         8.65        19.66         8.88        11.57        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 
       68.15       113.33        58.36        27.02        34.95        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       32.45        74.27       101.79        21.96        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       66.18       113.98        51.25        67.46        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       47.64        28.18        58.88        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I 
       30.38        15.58        22.55        35.44         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       42.94        14.76        12.36        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        77.79        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       53.36        60.99         1.64        14.53        13.28        10.13 

  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
           6.44            0.72 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
          43.66          165.17 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
          9.995          29.935 
[1] "6.4 - 43.7 (10.0)"  "0.7 - 165.2 (29.9)"
[1] "hr="     "3300000"
D15V2, continuous
                 vv
clus               T2  T3  T4
  ZMYM3 MUTATED     1   5   0
  ZMYM3 WILD-TYPE 127 189   6
D15V3, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T2             1             127
  T3             5             189
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V4, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     3   2
  ZMYM3 WILD-TYPE 230  50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      3    2
  ZMYM3 WILD-TYPE  230   50
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0             3             230
  1             2              50
[1] 2 2
[1] FALSE
D15V5, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     2   2
  ZMYM3 WILD-TYPE 250  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      2    2
  ZMYM3 WILD-TYPE  250   34
     clus
vv    ZMYM3 MUTATED ZMYM3 WILD-TYPE
  NO              2             250
  YES             2              34
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     0   6
  ZMYM3 WILD-TYPE  10 316
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      0    6
  ZMYM3 WILD-TYPE   10  316
                                        clus
vv                                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             316
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM3 MUTATED     2   4   0   0
  ZMYM3 WILD-TYPE 219  81   4   9
D15V7, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  R0             2             219
  R1             4              81
  R2             0               4
  RX             0               9
[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"
D15V8, continuous
D15V9, continuous
D15V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM3 MUTATED       0                         0     3
  ZMYM3 WILD-TYPE     2                         7   130
D15V11, multiclass
                           clus
vv                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             130
[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"

Clustering(16) Variable = AMFR MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  AMFR MUTATED     2   0
  AMFR WILD-TYPE 321   7
  AMFR MUTATED AMFR WILD-TYPE 
             2            328 
  AMFR MUTATED AMFR WILD-TYPE 
             0              7 
$`AMFR MUTATED`
TCGA-EJ-7125 TCGA-G9-6351 
       93.70        67.33 

$`AMFR WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        38.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        60.10        49.74        88.34        84.56 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.76        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G 
       76.41        38.10        24.85        25.18        20.58        21.96 
TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       21.96        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 
       55.76        49.81        50.70        47.15        46.52        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81        64.01        40.18        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 
       31.50        37.97        25.15        27.29        58.22        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       38.96        27.91        30.97        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         4.14        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 
       38.17        44.55         0.72         2.10        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 
        1.68        24.59        26.04         1.97        17.16        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       27.85        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W 
        1.15        22.36         0.76         1.78         2.01         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 
        4.93         9.53        25.48        18.84       109.25        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       43.69        20.19        40.04         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       16.83        22.52        10.78        14.37        20.28        13.87 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.55        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA 
       59.67        44.35        43.66        21.86         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
        8.88        11.57        83.34        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP 
       48.76        72.26       165.17        68.15       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.95        29.56        32.45        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
      101.79        21.96        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 
       51.25        67.46        20.65         5.19        12.62        13.15 
TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG 
       18.84        86.14        18.12         0.89        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       58.88        14.73        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       22.55        35.44         6.64         8.84        25.51        24.53 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       25.18        15.81        41.42        44.91        25.78       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58       102.90        23.93        89.49        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        58.32        42.94        14.76 
TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB 
       12.36        38.04        48.03         9.04         4.80        25.32 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       75.75        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       77.79        68.48         8.98        14.04        53.36        60.99 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        1.64        14.53        13.28        10.13 

  AMFR MUTATED AMFR WILD-TYPE 
         67.33           0.72 
  AMFR MUTATED AMFR WILD-TYPE 
         93.70         165.17 
  AMFR MUTATED AMFR WILD-TYPE 
        80.515         28.800 
[1] "67.3 - 93.7 (80.5)" "0.7 - 165.2 (28.8)"
[1] "Remove cluster labels:" "AMFR MUTATED"          
D16V2, continuous
                vv
clus              T2  T3  T4
  AMFR MUTATED     2   1   0
  AMFR WILD-TYPE 126 193   6
D16V3, multiclass
    clus
vv   AMFR MUTATED AMFR WILD-TYPE
  T2            2            126
  T3            1            193
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V4, binary
                cls
clus               0   1
  AMFR MUTATED     1   0
  AMFR WILD-TYPE 232  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMFR MUTATED      1    0
  AMFR WILD-TYPE  232   52
   clus
vv  AMFR MUTATED AMFR WILD-TYPE
  0            1            232
  1            0             52
[1] 2 2
[1] FALSE
D16V5, binary
                cls
clus               0   1
  AMFR MUTATED     1   1
  AMFR WILD-TYPE 251  35
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMFR MUTATED      1    1
  AMFR WILD-TYPE  251   35
     clus
vv    AMFR MUTATED AMFR WILD-TYPE
  NO             1            251
  YES            1             35
[1] 2 2
[1] FALSE
D16V6, binary
                cls
clus               0   1
  AMFR MUTATED     0   3
  AMFR WILD-TYPE  10 319
[1] "tbl2"
                cls
clus             [,1] [,2]
  AMFR MUTATED      0    3
  AMFR WILD-TYPE   10  319
                                        clus
vv                                       AMFR MUTATED AMFR WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            319
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AMFR MUTATED     2   1   0   0
  AMFR WILD-TYPE 219  84   4   9
D16V7, multiclass
    clus
vv   AMFR MUTATED AMFR WILD-TYPE
  R0            2            219
  R1            1             84
  R2            0              4
  RX            0              9
[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"
D16V8, continuous
[1] "Remove cluster labels:" "AMFR MUTATED"          
clus
  AMFR MUTATED AMFR WILD-TYPE 
             1            272 
    TCGA-2A-A8VL     TCGA-2A-A8VT     TCGA-2A-A8VV     TCGA-2A-A8W1 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-2A-A8W3     TCGA-CH-5737     TCGA-CH-5739     TCGA-CH-5740 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5744     TCGA-CH-5746     TCGA-CH-5748 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503     TCGA-EJ-5504 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7218     TCGA-EJ-7314 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8472     TCGA-EJ-8474 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-A46D     TCGA-EJ-A46G     TCGA-EJ-A65E     TCGA-EJ-A65F 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-A65G     TCGA-EJ-A65J     TCGA-EJ-A6RA     TCGA-EJ-A6RC 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-A7NF     TCGA-EJ-A7NG     TCGA-EJ-A7NJ     TCGA-EJ-A7NK 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-EJ-A7NM     TCGA-EJ-A8FN     TCGA-EJ-A8FS     TCGA-EJ-A8FU 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-FC-A5OB     TCGA-FC-A8O0 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6348     TCGA-G9-6356 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6370     TCGA-G9-6377     TCGA-G9-6384 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-G9-7522     TCGA-G9-7523     TCGA-HC-7078     TCGA-HC-7079 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7233 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740     TCGA-HC-7742 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-8258     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8264 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-8265     TCGA-HC-8266     TCGA-HC-A48F     TCGA-HC-A4ZV 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-A631     TCGA-HC-A632     TCGA-HC-A76W     TCGA-HC-A76X 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HC-A8CY     TCGA-HC-A8D0     TCGA-HC-A8D1     TCGA-HI-7168 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171     TCGA-J4-8200     TCGA-J4-A6G1 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-J4-A6G3     TCGA-J4-A83I     TCGA-J4-A83M     TCGA-J9-A52B 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-J9-A8CM     TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BR 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KC-A4BV     TCGA-KC-A7F3     TCGA-KC-A7F6     TCGA-KC-A7FA 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KC-A7FD     TCGA-KC-A7FE     TCGA-KK-A59X     TCGA-KK-A59Y 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KK-A59Z     TCGA-KK-A6DY     TCGA-KK-A6E0     TCGA-KK-A6E1 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KK-A6E2     TCGA-KK-A6E5     TCGA-KK-A6E6     TCGA-KK-A7AP 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KK-A7AU     TCGA-KK-A7AV     TCGA-KK-A7B1     TCGA-KK-A7B3 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KK-A7B4     TCGA-KK-A8I4     TCGA-KK-A8I6     TCGA-KK-A8IA 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-KK-A8ID     TCGA-KK-A8IJ     TCGA-KK-A8IL     TCGA-M7-A725 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-QU-A6IP     TCGA-SU-A7E7     TCGA-V1-A8MF     TCGA-V1-A8MJ 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-V1-A8ML     TCGA-V1-A8MU     TCGA-V1-A8WL     TCGA-V1-A8WV 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-V1-A8WW     TCGA-V1-A8X3     TCGA-VN-A88I     TCGA-VN-A88K 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-VN-A88L     TCGA-VN-A88N     TCGA-VN-A88O     TCGA-VN-A88P 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-VN-A88Q     TCGA-VN-A88R     TCGA-VP-A872     TCGA-VP-A875 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-VP-A876     TCGA-VP-A878     TCGA-VP-A879     TCGA-VP-A87B 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-VP-A87C     TCGA-VP-A87D     TCGA-VP-A87E     TCGA-VP-A87H 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-VP-A87J     TCGA-VP-A87K     TCGA-WW-A8ZI     TCGA-XA-A8JR 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-XJ-A83G     TCGA-XJ-A9DI     TCGA-XQ-A8TB     TCGA-Y6-A8TL 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-YJ-A8SW     TCGA-YL-A8HK     TCGA-YL-A8HL     TCGA-YL-A8HM 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-YL-A8HO     TCGA-YL-A8S8     TCGA-YL-A8S9     TCGA-YL-A8SA 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-YL-A8SB     TCGA-YL-A8SC     TCGA-YL-A8SF     TCGA-YL-A8SH 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-YL-A8SJ     TCGA-YL-A8SK     TCGA-YL-A8SL     TCGA-YL-A8SQ 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-YL-A8SR     TCGA-YL-A9WH     TCGA-YL-A9WI     TCGA-YL-A9WJ 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
    TCGA-ZG-A8QW     TCGA-ZG-A8QX     TCGA-ZG-A8QY     TCGA-ZG-A8QZ 
"AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" "AMFR WILD-TYPE" 
D16V9, continuous
D16V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMFR MUTATED       0                         1     2
  AMFR WILD-TYPE     2                         6   131
D16V11, multiclass
                           clus
vv                          AMFR MUTATED AMFR WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                                2            131
[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"

Clustering(17) Variable = IL6ST MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  IL6ST MUTATED     3   0
  IL6ST WILD-TYPE 320   7
  IL6ST MUTATED IL6ST WILD-TYPE 
              3             327 
  IL6ST MUTATED IL6ST WILD-TYPE 
              0               7 
$`IL6ST MUTATED`
TCGA-EJ-5526 TCGA-KK-A59X TCGA-VP-A878 
       38.76        83.34       102.90 

$`IL6ST WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       74.93        68.35        61.87        36.66        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        60.10        49.74        88.34        84.56        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.76        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G 
       76.41        38.10        24.85        25.18        20.58        21.96 
TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       21.96        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       55.76        49.81        67.33        50.70        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 
       45.30        39.39        44.81        64.01        40.18        38.01 
TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       40.31        31.50        37.97        25.15        27.29        58.22 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.44        28.18 
TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        6.08        19.76        65.26         4.14        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 
        2.37        38.17        44.55         0.72         2.10        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        24.59        26.04         1.97        17.16 
TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       23.87        27.85        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84       109.25 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 
       82.92        43.69        20.19        40.04         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N 
       27.91        16.83        22.52        10.78        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
       13.87        10.55        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       30.71        59.67        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY 
       19.66         8.88        11.57        64.70        86.40       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP 
       48.76        72.26       165.17        68.15       113.33         6.44 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       58.36        27.02        34.95        29.56        32.45        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
      101.79        21.96        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 
       51.25        67.46        20.65         5.19        12.62        13.15 
TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG 
       18.84        86.14        18.12         0.89        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       58.88        14.73        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       22.55        35.44         6.64         8.84        25.51        24.53 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       25.18        15.81        41.42        44.91        25.78       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       75.91       109.58        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR 
       66.97        21.80        58.32        42.94        14.76        12.36 
TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       38.04        48.03         9.04         4.80        25.32        32.61 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        75.75 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW 
       68.48         8.98        14.04        53.36        60.99         1.64 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  IL6ST MUTATED IL6ST WILD-TYPE 
          38.76            0.72 
  IL6ST MUTATED IL6ST WILD-TYPE 
         102.90          165.17 
  IL6ST MUTATED IL6ST WILD-TYPE 
          83.34           28.77 
[1] "38.8 - 102.9 (83.3)" "0.7 - 165.2 (28.8)" 
[1] "hr="     "9200000"
D17V2, continuous
                 vv
clus               T2  T3  T4
  IL6ST MUTATED     1   2   0
  IL6ST WILD-TYPE 127 192   6
D17V3, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  T2             1             127
  T3             2             192
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V4, binary
                 cls
clus                0   1
  IL6ST MUTATED     0   3
  IL6ST WILD-TYPE 233  49
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      0    3
  IL6ST WILD-TYPE  233   49
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             0             233
  1             3              49
[1] 2 2
[1] FALSE
D17V5, binary
                 cls
clus                0   1
  IL6ST MUTATED     2   1
  IL6ST WILD-TYPE 250  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      2    1
  IL6ST WILD-TYPE  250   35
     clus
vv    IL6ST MUTATED IL6ST WILD-TYPE
  NO              2             250
  YES             1              35
[1] 2 2
[1] FALSE
D17V6, binary
                 cls
clus                0   1
  IL6ST MUTATED     0   3
  IL6ST WILD-TYPE  10 319
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      0    3
  IL6ST WILD-TYPE   10  319
                                        clus
vv                                       IL6ST MUTATED IL6ST WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             319
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  IL6ST MUTATED     1   2   0   0
  IL6ST WILD-TYPE 220  83   4   9
D17V7, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  R0             1             220
  R1             2              83
  R2             0               4
  RX             0               9
[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"
D17V8, continuous
D17V9, continuous
D17V10, continuous
[1] "Remove cluster labels:" "IL6ST MUTATED"         
clus
  IL6ST MUTATED IL6ST WILD-TYPE 
              2             295 
     TCGA-2A-A8VL      TCGA-2A-A8VO      TCGA-2A-A8VT      TCGA-2A-A8VV 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-2A-A8W1      TCGA-2A-A8W3      TCGA-CH-5737      TCGA-CH-5738 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5739      TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5744 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5495 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5527      TCGA-EJ-5530 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7218      TCGA-EJ-7314 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7318      TCGA-EJ-7321 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7791      TCGA-EJ-7792 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-8469      TCGA-EJ-8472      TCGA-EJ-8474      TCGA-EJ-A46D 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-A46G      TCGA-EJ-A46I      TCGA-EJ-A65E      TCGA-EJ-A65F 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-A65G      TCGA-EJ-A65J      TCGA-EJ-A6RA      TCGA-EJ-A6RC 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-A7NF      TCGA-EJ-A7NG      TCGA-EJ-A7NH      TCGA-EJ-A7NJ 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-A7NK      TCGA-EJ-A7NM      TCGA-EJ-A8FN      TCGA-EJ-A8FS 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-FC-A8O0      TCGA-G9-6329      TCGA-G9-6333 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6342      TCGA-G9-6348      TCGA-G9-6351 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6363 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6377      TCGA-G9-6378 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6499 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-7523      TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7209 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7230      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7740 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7818      TCGA-HC-7821      TCGA-HC-8216 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-8257      TCGA-HC-8258      TCGA-HC-8260      TCGA-HC-8262 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-8265      TCGA-HC-A76W      TCGA-HC-A76X      TCGA-HC-A8CY 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-A8D0      TCGA-HC-A8D1      TCGA-HI-7168      TCGA-HI-7170 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HI-7171      TCGA-J4-8198      TCGA-J4-8200      TCGA-J4-A67T 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-J4-A6G1      TCGA-J4-A6G3      TCGA-J4-A6M7      TCGA-J4-A83I 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-J4-A83K      TCGA-J4-A83M      TCGA-J4-A83N      TCGA-J9-A52B 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-J9-A8CK      TCGA-J9-A8CL      TCGA-J9-A8CM      TCGA-J9-A8CN 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-J9-A8CP      TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BR 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KC-A7F3      TCGA-KC-A7F6      TCGA-KC-A7FA 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KC-A7FD      TCGA-KC-A7FE      TCGA-KK-A59Y      TCGA-KK-A59Z 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A6DY      TCGA-KK-A6E0      TCGA-KK-A6E1      TCGA-KK-A6E2 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A7AU      TCGA-KK-A7AV 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A7B1      TCGA-KK-A7B3      TCGA-KK-A7B4      TCGA-KK-A8I4 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A8I5      TCGA-KK-A8I6      TCGA-KK-A8I8      TCGA-KK-A8I9 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A8IA      TCGA-KK-A8IC      TCGA-KK-A8ID      TCGA-KK-A8IF 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A8IG      TCGA-KK-A8IH      TCGA-KK-A8II      TCGA-KK-A8IJ 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-KK-A8IK      TCGA-KK-A8IL      TCGA-QU-A6IP      TCGA-SU-A7E7 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-V1-A8MF      TCGA-V1-A8MG      TCGA-V1-A8MJ      TCGA-V1-A8ML 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-V1-A8MU      TCGA-V1-A8WL      TCGA-V1-A8WN      TCGA-V1-A8WS 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-V1-A8WV      TCGA-V1-A8WW      TCGA-V1-A8X3      TCGA-VN-A88I 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-VN-A88K      TCGA-VN-A88L      TCGA-VN-A88N      TCGA-VN-A88O 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-VN-A88P      TCGA-VN-A88Q      TCGA-VN-A88R      TCGA-VP-A872 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-VP-A875      TCGA-VP-A876      TCGA-VP-A879      TCGA-VP-A87B 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-VP-A87C      TCGA-VP-A87D      TCGA-VP-A87E      TCGA-VP-A87H 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-VP-A87J      TCGA-VP-A87K      TCGA-WW-A8ZI      TCGA-XA-A8JR 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-XJ-A83G      TCGA-XJ-A83H      TCGA-XJ-A9DI      TCGA-XJ-A9DK 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-XQ-A8TA      TCGA-XQ-A8TB      TCGA-Y6-A8TL      TCGA-YJ-A8SW 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A8HJ      TCGA-YL-A8HK      TCGA-YL-A8HL      TCGA-YL-A8HM 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A8HO      TCGA-YL-A8S8      TCGA-YL-A8S9      TCGA-YL-A8SA 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A8SB      TCGA-YL-A8SC      TCGA-YL-A8SF      TCGA-YL-A8SH 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A8SJ      TCGA-YL-A8SK      TCGA-YL-A8SL      TCGA-YL-A8SO 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A8SP      TCGA-YL-A8SQ      TCGA-YL-A8SR      TCGA-YL-A9WH 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-YL-A9WI      TCGA-YL-A9WJ      TCGA-ZG-A8QZ 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL6ST MUTATED       0                         0     1
  IL6ST WILD-TYPE     2                         7   132
D17V11, multiclass
[1] "Remove cluster labels:" "IL6ST MUTATED"         
clus
  IL6ST MUTATED IL6ST WILD-TYPE 
              1             141 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5744      TCGA-CH-5746      TCGA-CH-5748 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6329      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6342 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6370      TCGA-G9-6371 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7747 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7818 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7170 
"IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" "IL6ST WILD-TYPE" 
     TCGA-HI-7171 
"IL6ST WILD-TYPE" 

Clustering(18) Variable = CDK12 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     6   0
  CDK12 WILD-TYPE 317   7
  CDK12 MUTATED CDK12 WILD-TYPE 
              6             324 
  CDK12 MUTATED CDK12 WILD-TYPE 
              0               7 
$`CDK12 MUTATED`
TCGA-CH-5739 TCGA-EJ-7784 TCGA-EJ-A46G TCGA-HC-8265 TCGA-KK-A59X TCGA-KK-A8ID 
       22.06        25.68        21.96        15.88        83.34        69.27 

$`CDK12 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        2.99         6.97         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
        1.02        13.02        35.01        31.00         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        61.87        36.66        38.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        60.10        49.74        88.34        84.56        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       83.57        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        38.70        36.03        28.24        36.33        36.76 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       45.90         3.75        42.94        32.32        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46I TCGA-EJ-A65E 
       38.10        24.85        25.18        20.58        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN 
       14.20        15.58         6.48        15.65         4.21        10.82 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        28.83        22.36 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 
       20.25        41.62        81.04        67.99        55.76        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       67.33        50.70        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 
       44.81        64.01        40.18        38.01        40.31        31.50 
TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 
       37.97        25.15        27.29        58.22        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 
       27.91        30.97        35.44        28.18         6.08        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         4.14        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         0.72         2.10        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       24.59        26.04         1.97        17.16        30.84        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8266 TCGA-HC-A48F 
       22.55        17.95        22.32         1.58         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        0.76         1.78         2.01         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       64.70        86.40       141.21        48.76        72.26       165.17 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 
       68.15       113.33         6.44        58.36        27.02        34.95 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 
       29.56        32.45        74.27       101.79        21.96        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48         2.73        67.43        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       66.18       113.98        51.25        67.46        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       47.64        28.18        58.88        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I 
       30.38        15.58        22.55        35.44         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       119.38        75.91       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       42.94        14.76        12.36        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        77.79        68.48         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       53.36        60.99         1.64        14.53        13.28        10.13 

  CDK12 MUTATED CDK12 WILD-TYPE 
          15.88            0.72 
  CDK12 MUTATED CDK12 WILD-TYPE 
          83.34          165.17 
  CDK12 MUTATED CDK12 WILD-TYPE 
          23.87           29.28 
[1] "15.9 - 83.3 (23.9)" "0.7 - 165.2 (29.3)"
[1] "hr="     "9200000"
D18V2, continuous
                 vv
clus               T2  T3  T4
  CDK12 MUTATED     1   5   0
  CDK12 WILD-TYPE 127 189   6
D18V3, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T2             1             127
  T3             5             189
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V4, binary
                 cls
clus                0   1
  CDK12 MUTATED     4   2
  CDK12 WILD-TYPE 229  50
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      4    2
  CDK12 WILD-TYPE  229   50
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0             4             229
  1             2              50
[1] 2 2
[1] FALSE
D18V5, binary
                 cls
clus                0   1
  CDK12 MUTATED     4   2
  CDK12 WILD-TYPE 248  34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      4    2
  CDK12 WILD-TYPE  248   34
     clus
vv    CDK12 MUTATED CDK12 WILD-TYPE
  NO              4             248
  YES             2              34
[1] 2 2
[1] FALSE
D18V6, binary
                 cls
clus                0   1
  CDK12 MUTATED     1   5
  CDK12 WILD-TYPE   9 317
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      1    5
  CDK12 WILD-TYPE    9  317
                                        clus
vv                                       CDK12 MUTATED CDK12 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1               9
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             317
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED     3   3   0   0
  CDK12 WILD-TYPE 218  82   4   9
D18V7, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0             3             218
  R1             3              82
  R2             0               4
  RX             0               9
[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"
D18V8, continuous
D18V9, continuous
D18V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED       0                         0     2
  CDK12 WILD-TYPE     2                         7   131
D18V11, multiclass
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              2             140 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5740      TCGA-CH-5741 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5744      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6342      TCGA-G9-6348 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6367      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6377 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231      TCGA-HC-7232 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7740 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7747      TCGA-HC-7748 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7818      TCGA-HC-7820 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7170      TCGA-HI-7171 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 

Clustering(19) Variable = NKX3-1 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  NKX3-1 MUTATED     4   0
  NKX3-1 WILD-TYPE 319   7
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               4              326 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               0                7 
$`NKX3-1 MUTATED`
TCGA-CH-5767 TCGA-CH-5794 TCGA-EJ-5517 TCGA-EJ-5530 
       15.06        29.00        62.10        60.23 

$`NKX3-1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
        1.02        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-EJ-5494 TCGA-EJ-5495 
        9.99        32.02        33.01         2.99        48.56        57.86 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.56        13.32        56.55        46.52        44.88        38.50 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       45.73        46.92        30.31        45.40        47.90        64.60 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       48.13        62.04        48.53        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        69.63        64.50        74.93        68.35        61.87 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        58.45        41.85        60.10        49.74 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       88.34        84.56        93.70        83.57        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        35.28        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       36.03        28.24        36.33        36.76        45.90         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       42.94        32.32        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F 
       25.18        20.58        21.96        21.96        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90        14.83        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       15.58         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        0.72         2.10        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 
       26.04         1.97        17.16        30.84        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 
       19.36        22.42        28.27        23.87        27.85        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        0.76         1.78         2.01         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       25.48        18.84       109.25        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       40.04         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL 
       10.78        14.37        20.28        13.87        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR 
       15.22        40.67        12.69        30.71        59.67        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       83.34        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
      165.17        68.15       113.33         6.44        58.36        27.02 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        29.56        32.45        74.27       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP 
       20.65         5.19        12.62        13.15        18.84        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML 
       18.12         0.89        47.64        28.18        58.88        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        25.51        24.53        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
        8.98        14.04        53.36        60.99         1.64        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
           15.06             0.72 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
           62.10           165.17 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
          44.615           28.800 
[1] "15.1 - 62.1 (44.6)" "0.7 - 165.2 (28.8)"
[1] "hr="     "9100000"
D19V2, continuous
                  vv
clus                T2  T3  T4
  NKX3-1 MUTATED     4   0   0
  NKX3-1 WILD-TYPE 124 194   6
D19V3, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  T2              4              124
  T3              0              194
  T4              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V4, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     4   0
  NKX3-1 WILD-TYPE 229  52
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      4    0
  NKX3-1 WILD-TYPE  229   52
   clus
vv  NKX3-1 MUTATED NKX3-1 WILD-TYPE
  0              4              229
  1              0               52
[1] 2 2
[1] FALSE
D19V5, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     4   0
  NKX3-1 WILD-TYPE 248  36
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      4    0
  NKX3-1 WILD-TYPE  248   36
     clus
vv    NKX3-1 MUTATED NKX3-1 WILD-TYPE
  NO               4              248
  YES              0               36
[1] 2 2
[1] FALSE
D19V6, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     0   4
  NKX3-1 WILD-TYPE  10 318
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      0    4
  NKX3-1 WILD-TYPE   10  318
                                        clus
vv                                       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              318
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NKX3-1 MUTATED     4   0   0   0
  NKX3-1 WILD-TYPE 217  85   4   9
D19V7, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  R0              4              217
  R1              0               85
  R2              0                4
  RX              0                9
[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"
D19V8, continuous
D19V9, continuous
D19V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NKX3-1 MUTATED       0                         0     4
  NKX3-1 WILD-TYPE     2                         7   129
D19V11, multiclass
                           clus
vv                          NKX3-1 MUTATED NKX3-1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  4              129
[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"

Clustering(20) Variable = IRF4 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  IRF4 MUTATED     4   0
  IRF4 WILD-TYPE 319   7
  IRF4 MUTATED IRF4 WILD-TYPE 
             4            326 
  IRF4 MUTATED IRF4 WILD-TYPE 
             0              7 
$`IRF4 MUTATED`
TCGA-EJ-7327 TCGA-G9-6351 TCGA-HC-7081 TCGA-KK-A59X 
       30.35        67.33        37.35        83.34 

$`IRF4 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       48.56        57.86        19.56        13.32        56.55        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        38.50        45.73        46.92        30.31        45.40 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       47.90        64.60        48.13        62.04        48.53        56.98 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       60.13        60.23        62.10        62.10        69.63        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        38.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        60.10        49.74        88.34        84.56 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       93.70        83.57        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       27.09        27.68         6.28        24.39        35.28        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        38.70        36.03        28.24        36.33 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.76        45.90         3.75        42.94        32.32        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G 
       76.41        38.10        24.85        25.18        20.58        21.96 
TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       21.96        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        4.21        10.82         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 
       28.83        22.36        20.25        41.62        81.04        67.99 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 
       55.76        49.81        50.70        47.15        46.52        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81        64.01        40.18        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 
       31.50        37.97        25.15        27.29        58.22        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 
       38.96        27.91        30.97        35.44        28.18         6.08 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 
       19.76        65.26         4.14        36.36        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         0.72         2.10        23.57         1.48         1.68 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 
       24.59        26.04         1.97        17.16        30.84        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X 
       22.36         0.76         1.78         2.01         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
        9.53        25.48        18.84       109.25        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       20.19        40.04         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK 
       22.52        10.78        14.37        20.28        13.87        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       44.35        43.66        21.86         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       11.57        64.70        86.40       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV 
      165.17        68.15       113.33         6.44        58.36        27.02 
TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        29.56        32.45        74.27       101.79        21.96 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP 
       20.65         5.19        12.62        13.15        18.84        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML 
       18.12         0.89        47.64        28.18        58.88        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        25.51        24.53        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       119.38        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      102.90        23.93        89.49        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G 
       21.80        58.32        42.94        14.76        12.36        38.04 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         4.80        25.32        32.61         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        75.75        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        77.79        68.48 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
        8.98        14.04        53.36        60.99         1.64        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  IRF4 MUTATED IRF4 WILD-TYPE 
         30.35           0.72 
  IRF4 MUTATED IRF4 WILD-TYPE 
         83.34         165.17 
  IRF4 MUTATED IRF4 WILD-TYPE 
        52.340         28.735 
[1] "30.4 - 83.3 (52.3)" "0.7 - 165.2 (28.7)"
[1] "hr="     "9200000"
D20V2, continuous
                vv
clus              T2  T3  T4
  IRF4 MUTATED     1   3   0
  IRF4 WILD-TYPE 127 191   6
D20V3, multiclass
    clus
vv   IRF4 MUTATED IRF4 WILD-TYPE
  T2            1            127
  T3            3            191
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V4, binary
                cls
clus               0   1
  IRF4 MUTATED     1   1
  IRF4 WILD-TYPE 232  51
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF4 MUTATED      1    1
  IRF4 WILD-TYPE  232   51
   clus
vv  IRF4 MUTATED IRF4 WILD-TYPE
  0            1            232
  1            1             51
[1] 2 2
[1] FALSE
D20V5, binary
                cls
clus               0   1
  IRF4 MUTATED     1   3
  IRF4 WILD-TYPE 251  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF4 MUTATED      1    3
  IRF4 WILD-TYPE  251   33
     clus
vv    IRF4 MUTATED IRF4 WILD-TYPE
  NO             1            251
  YES            3             33
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus               0   1
  IRF4 MUTATED     0   4
  IRF4 WILD-TYPE  10 318
[1] "tbl2"
                cls
clus             [,1] [,2]
  IRF4 MUTATED      0    4
  IRF4 WILD-TYPE   10  318
                                        clus
vv                                       IRF4 MUTATED IRF4 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             10
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            318
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IRF4 MUTATED     1   2   1   0
  IRF4 WILD-TYPE 220  83   3   9
D20V7, multiclass
    clus
vv   IRF4 MUTATED IRF4 WILD-TYPE
  R0            1            220
  R1            2             83
  R2            1              3
  RX            0              9
[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"
D20V8, continuous
[1] "Remove cluster labels:" "IRF4 MUTATED"          
clus
  IRF4 MUTATED IRF4 WILD-TYPE 
             2            271 
    TCGA-2A-A8VL     TCGA-2A-A8VT     TCGA-2A-A8VV     TCGA-2A-A8W1 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-2A-A8W3     TCGA-CH-5737     TCGA-CH-5739     TCGA-CH-5740 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5744     TCGA-CH-5746     TCGA-CH-5748 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503     TCGA-EJ-5504 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7218 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8472     TCGA-EJ-8474 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A46D     TCGA-EJ-A46G     TCGA-EJ-A65E     TCGA-EJ-A65F 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A65G     TCGA-EJ-A65J     TCGA-EJ-A6RA     TCGA-EJ-A6RC 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A7NF     TCGA-EJ-A7NG     TCGA-EJ-A7NJ     TCGA-EJ-A7NK 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A7NM     TCGA-EJ-A8FN     TCGA-EJ-A8FS     TCGA-EJ-A8FU 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-FC-A5OB     TCGA-FC-A8O0 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6348     TCGA-G9-6356 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6370     TCGA-G9-6377     TCGA-G9-6384 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-7522     TCGA-G9-7523     TCGA-HC-7078     TCGA-HC-7079 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7233 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740     TCGA-HC-7742 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-8258     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8264 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-8265     TCGA-HC-8266     TCGA-HC-A48F     TCGA-HC-A4ZV 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-A631     TCGA-HC-A632     TCGA-HC-A76W     TCGA-HC-A76X 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-A8CY     TCGA-HC-A8D0     TCGA-HC-A8D1     TCGA-HI-7168 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171     TCGA-J4-8200     TCGA-J4-A6G1 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J4-A6G3     TCGA-J4-A83I     TCGA-J4-A83M     TCGA-J9-A52B 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J9-A8CM     TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BR 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KC-A4BV     TCGA-KC-A7F3     TCGA-KC-A7F6     TCGA-KC-A7FA 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KC-A7FD     TCGA-KC-A7FE     TCGA-KK-A59Y     TCGA-KK-A59Z 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A6DY     TCGA-KK-A6E0     TCGA-KK-A6E1     TCGA-KK-A6E2 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A6E5     TCGA-KK-A6E6     TCGA-KK-A7AP     TCGA-KK-A7AU 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A7AV     TCGA-KK-A7B1     TCGA-KK-A7B3     TCGA-KK-A7B4 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8I4     TCGA-KK-A8I6     TCGA-KK-A8IA     TCGA-KK-A8ID 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8IJ     TCGA-KK-A8IL     TCGA-M7-A725     TCGA-QU-A6IP 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-SU-A7E7     TCGA-V1-A8MF     TCGA-V1-A8MJ     TCGA-V1-A8ML 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-V1-A8MU     TCGA-V1-A8WL     TCGA-V1-A8WV     TCGA-V1-A8WW 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-V1-A8X3     TCGA-VN-A88I     TCGA-VN-A88K     TCGA-VN-A88L 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VN-A88N     TCGA-VN-A88O     TCGA-VN-A88P     TCGA-VN-A88Q 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VN-A88R     TCGA-VP-A872     TCGA-VP-A875     TCGA-VP-A876 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A878     TCGA-VP-A879     TCGA-VP-A87B     TCGA-VP-A87C 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A87D     TCGA-VP-A87E     TCGA-VP-A87H     TCGA-VP-A87J 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A87K     TCGA-WW-A8ZI     TCGA-XA-A8JR     TCGA-XJ-A83G 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-XJ-A9DI     TCGA-XQ-A8TB     TCGA-Y6-A8TL     TCGA-YJ-A8SW 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8HK     TCGA-YL-A8HL     TCGA-YL-A8HM     TCGA-YL-A8HO 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8S8     TCGA-YL-A8S9     TCGA-YL-A8SA     TCGA-YL-A8SB 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8SC     TCGA-YL-A8SF     TCGA-YL-A8SH     TCGA-YL-A8SJ 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8SK     TCGA-YL-A8SL     TCGA-YL-A8SQ     TCGA-YL-A8SR 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A9WH     TCGA-YL-A9WI     TCGA-YL-A9WJ     TCGA-ZG-A8QW 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-ZG-A8QX     TCGA-ZG-A8QY     TCGA-ZG-A8QZ 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
D20V9, continuous
D20V10, continuous
[1] "Remove cluster labels:" "IRF4 MUTATED"          
clus
  IRF4 MUTATED IRF4 WILD-TYPE 
             2            295 
    TCGA-2A-A8VL     TCGA-2A-A8VO     TCGA-2A-A8VT     TCGA-2A-A8VV 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-2A-A8W1     TCGA-2A-A8W3     TCGA-CH-5737     TCGA-CH-5738 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5739     TCGA-CH-5740     TCGA-CH-5741     TCGA-CH-5744 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5495 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5502     TCGA-EJ-5503     TCGA-EJ-5504 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7218 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7318 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7791     TCGA-EJ-7792 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-EJ-8468 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-8469     TCGA-EJ-8472     TCGA-EJ-8474     TCGA-EJ-A46D 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A46G     TCGA-EJ-A46I     TCGA-EJ-A65E     TCGA-EJ-A65F 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A65G     TCGA-EJ-A65J     TCGA-EJ-A6RA     TCGA-EJ-A6RC 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A7NF     TCGA-EJ-A7NG     TCGA-EJ-A7NH     TCGA-EJ-A7NJ 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-EJ-A7NK     TCGA-EJ-A7NM     TCGA-EJ-A8FN     TCGA-EJ-A8FS 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-FC-A5OB     TCGA-FC-A8O0     TCGA-G9-6329     TCGA-G9-6333 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6336     TCGA-G9-6342     TCGA-G9-6348     TCGA-G9-6353 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6363     TCGA-G9-6364 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6370 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6371     TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-6385     TCGA-G9-6494     TCGA-G9-6499     TCGA-G9-7510 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-G9-7519     TCGA-G9-7521     TCGA-G9-7522     TCGA-G9-7523 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-H9-7775     TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740     TCGA-HC-7744 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7750 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-8258     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8265 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-A76W     TCGA-HC-A76X     TCGA-HC-A8CY     TCGA-HC-A8D0 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-HC-A8D1     TCGA-HI-7168     TCGA-HI-7170     TCGA-HI-7171 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J4-8198     TCGA-J4-8200     TCGA-J4-A67T     TCGA-J4-A6G1 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J4-A6G3     TCGA-J4-A6M7     TCGA-J4-A83I     TCGA-J4-A83K 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J4-A83M     TCGA-J4-A83N     TCGA-J9-A52B     TCGA-J9-A8CK 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-J9-A8CL     TCGA-J9-A8CM     TCGA-J9-A8CN     TCGA-J9-A8CP 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BR     TCGA-KC-A4BV 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KC-A7F3     TCGA-KC-A7F6     TCGA-KC-A7FA     TCGA-KC-A7FD 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KC-A7FE     TCGA-KK-A59Y     TCGA-KK-A59Z     TCGA-KK-A6DY 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A6E0     TCGA-KK-A6E1     TCGA-KK-A6E2     TCGA-KK-A6E5 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A6E6     TCGA-KK-A7AU     TCGA-KK-A7AV     TCGA-KK-A7B1 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A7B3     TCGA-KK-A7B4     TCGA-KK-A8I4     TCGA-KK-A8I5 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8I6     TCGA-KK-A8I8     TCGA-KK-A8I9     TCGA-KK-A8IA 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8IC     TCGA-KK-A8ID     TCGA-KK-A8IF     TCGA-KK-A8IG 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8IH     TCGA-KK-A8II     TCGA-KK-A8IJ     TCGA-KK-A8IK 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-KK-A8IL     TCGA-QU-A6IP     TCGA-SU-A7E7     TCGA-V1-A8MF 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-V1-A8MG     TCGA-V1-A8MJ     TCGA-V1-A8ML     TCGA-V1-A8MU 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-V1-A8WL     TCGA-V1-A8WN     TCGA-V1-A8WS     TCGA-V1-A8WV 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-V1-A8WW     TCGA-V1-A8X3     TCGA-VN-A88I     TCGA-VN-A88K 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VN-A88L     TCGA-VN-A88N     TCGA-VN-A88O     TCGA-VN-A88P 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VN-A88Q     TCGA-VN-A88R     TCGA-VP-A872     TCGA-VP-A875 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A876     TCGA-VP-A878     TCGA-VP-A879     TCGA-VP-A87B 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A87C     TCGA-VP-A87D     TCGA-VP-A87E     TCGA-VP-A87H 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-VP-A87J     TCGA-VP-A87K     TCGA-WW-A8ZI     TCGA-XA-A8JR 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-XJ-A83G     TCGA-XJ-A83H     TCGA-XJ-A9DI     TCGA-XJ-A9DK 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-XQ-A8TA     TCGA-XQ-A8TB     TCGA-Y6-A8TL     TCGA-YJ-A8SW 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8HJ     TCGA-YL-A8HK     TCGA-YL-A8HL     TCGA-YL-A8HM 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8HO     TCGA-YL-A8S8     TCGA-YL-A8S9     TCGA-YL-A8SA 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8SB     TCGA-YL-A8SC     TCGA-YL-A8SF     TCGA-YL-A8SH 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8SJ     TCGA-YL-A8SK     TCGA-YL-A8SL     TCGA-YL-A8SO 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A8SP     TCGA-YL-A8SQ     TCGA-YL-A8SR     TCGA-YL-A9WH 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
    TCGA-YL-A9WI     TCGA-YL-A9WJ     TCGA-ZG-A8QZ 
"IRF4 WILD-TYPE" "IRF4 WILD-TYPE" "IRF4 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IRF4 MUTATED       0                         0     3
  IRF4 WILD-TYPE     2                         7   130
D20V11, multiclass
                           clus
vv                          IRF4 MUTATED IRF4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            130
[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"

Clustering(21) Variable = ASH1L MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ASH1L MUTATED     7   0
  ASH1L WILD-TYPE 316   7
  ASH1L MUTATED ASH1L WILD-TYPE 
              7             323 
  ASH1L MUTATED ASH1L WILD-TYPE 
              0               7 
$`ASH1L MUTATED`
TCGA-CH-5739 TCGA-CH-5752 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5505 TCGA-EJ-A8FS 
       22.06        31.00        48.56        57.86        30.31         8.75 
TCGA-V1-A8ML 
       14.73 

$`ASH1L WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 TCGA-CH-5746 
        2.99         6.97         1.02        12.99         1.97        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        35.01         1.02         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        13.02        15.98        26.99         9.99 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5496 TCGA-EJ-5497 
       32.02        33.01         2.99        29.00        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       56.55        46.52        44.88        38.50        45.73        46.92 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       45.40        47.90        64.60        48.13        62.04        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       56.98        60.13        60.23        62.10        62.10        69.63 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        74.93        68.35        61.87        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       58.45        60.23        41.85        60.10        49.74        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       84.56        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        27.09        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       35.28        38.37        25.87        25.68        38.70        36.03 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       28.24        36.33        36.76        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       32.32        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       20.58        21.96        21.96        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FU TCGA-FC-7708 
        6.48        15.65         4.21        10.82         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6333 
       15.42        28.83        22.36        20.25        41.62        81.04 
TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       67.99        55.76        49.81        67.33        50.70        47.15 
TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        45.30        39.39        44.81        64.01        40.18 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       38.01        40.31        31.50        37.97        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       58.22        50.73        38.96        27.91        30.97        35.44 
TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       28.18         6.08        19.76        65.26         4.14        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.48         1.68        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       17.16        30.84        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       28.27        23.87        27.85        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        2.01         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T 
      109.25        82.92        43.69        20.19        40.04         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
       25.28        27.91        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.87        10.55        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        30.71        59.67        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 
       86.40       141.21        48.76        72.26       165.17        68.15 
TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 
      113.33         6.44        58.36        27.02        34.95        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8I9 
       32.45        74.27       101.79        21.96        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-M7-A71Y 
       66.18       113.98        51.25        67.46        20.65         5.19 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
       12.62        13.15        18.84        86.14        18.12         0.89 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       47.64        28.18        58.88        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       15.58        22.55        35.44         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
       24.53        25.18        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      119.38        75.91       109.58       102.90        23.93        89.49 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        58.32        42.94 
TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XQ-A8TA 
       14.76        12.36        38.04        48.03         9.04         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       25.32        32.61         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        75.75        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        77.79        68.48         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         1.64        14.53        13.28        10.13 

  ASH1L MUTATED ASH1L WILD-TYPE 
           8.75            0.72 
  ASH1L MUTATED ASH1L WILD-TYPE 
          57.86          165.17 
  ASH1L MUTATED ASH1L WILD-TYPE 
          30.31           28.83 
[1] "8.8 - 57.9 (30.3)"  "0.7 - 165.2 (28.8)"
[1] "hr="     "9200000"
D21V2, continuous
                 vv
clus               T2  T3  T4
  ASH1L MUTATED     2   5   0
  ASH1L WILD-TYPE 126 189   6
D21V3, multiclass
    clus
vv   ASH1L MUTATED ASH1L WILD-TYPE
  T2             2             126
  T3             5             189
  T4             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V4, binary
                 cls
clus                0   1
  ASH1L MUTATED     6   1
  ASH1L WILD-TYPE 227  51
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      6    1
  ASH1L WILD-TYPE  227   51
   clus
vv  ASH1L MUTATED ASH1L WILD-TYPE
  0             6             227
  1             1              51
[1] 2 2
[1] FALSE
D21V5, binary
                 cls
clus                0   1
  ASH1L MUTATED     6   1
  ASH1L WILD-TYPE 246  35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      6    1
  ASH1L WILD-TYPE  246   35
     clus
vv    ASH1L MUTATED ASH1L WILD-TYPE
  NO              6             246
  YES             1              35
[1] 2 2
[1] FALSE
D21V6, binary
                 cls
clus                0   1
  ASH1L MUTATED     0   7
  ASH1L WILD-TYPE  10 315
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASH1L MUTATED      0    7
  ASH1L WILD-TYPE   10  315
                                        clus
vv                                       ASH1L MUTATED ASH1L WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              10
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             315
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ASH1L MUTATED     7   0   0   0
  ASH1L WILD-TYPE 214  85   4   9
D21V7, multiclass
    clus
vv   ASH1L MUTATED ASH1L WILD-TYPE
  R0             7             214
  R1             0              85
  R2             0               4
  RX             0               9
[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"
D21V8, continuous
D21V9, continuous
D21V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASH1L MUTATED       0                         0     5
  ASH1L WILD-TYPE     2                         7   128
D21V11, multiclass
                           clus
vv                          ASH1L MUTATED ASH1L WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 5             128
[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"

Clustering(22) Variable = MLL3 MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    11   2
  MLL3 WILD-TYPE 312   5
  MLL3 MUTATED MLL3 WILD-TYPE 
            13            317 
  MLL3 MUTATED MLL3 WILD-TYPE 
             2              5 
$`MLL3 MUTATED`
TCGA-CH-5752 TCGA-EJ-5524 TCGA-EJ-7123 TCGA-EJ-A7NH TCGA-HC-7233 TCGA-HI-7170 
       31.00        61.87        84.56        15.58        44.55        82.92 
TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8II TCGA-KK-A8IL TCGA-VN-A88L TCGA-VP-A875 
       32.91        26.43       113.98        20.65        24.53        75.91 
TCGA-YL-A9WH 
       14.04 

$`MLL3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        12.99         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        13.02        35.01         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        13.02        15.98        26.99 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.99        32.02        33.01         2.99        29.00        48.56 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       57.86        19.56        13.32        56.55        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       38.50        45.73        46.92        30.31        45.40        47.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       64.60        48.13        62.04        48.53        56.98        60.13 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        62.10        62.10        69.63        64.50        74.93 
TCGA-EJ-5522 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       68.35        36.66        38.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       60.10        49.74        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        35.28        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       38.70        36.03        28.24        36.33        36.76        45.90 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        42.94        32.32        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46G TCGA-EJ-A46I TCGA-EJ-A65E 
       24.85        25.18        20.58        21.96        21.96        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       18.41        21.90        14.83        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A8FN TCGA-EJ-A8FS 
       14.20         6.48        15.65         4.21        10.82         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A8O0 
        4.54        28.41        15.42        28.83        22.36        20.25 
TCGA-G9-6329 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 
       41.62        81.04        67.99        55.76        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       50.70        47.15        46.52        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       64.01        40.18        38.01        40.31        31.50        37.97 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       25.15        27.29        58.22        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-H9-7775 TCGA-HC-7075 TCGA-HC-7078 
       30.97        35.44        28.18         6.08        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        4.14        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08         1.68         2.37        38.17         0.72 
TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 TCGA-HC-7748 
        2.10        23.57         1.48         1.68        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7818 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
        1.97        17.16        30.84        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 
       22.42        28.27        23.87        27.85        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.78         2.01         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67T 
       18.84       109.25        43.69        20.19        40.04         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83M 
       25.28        27.91        16.83        22.52        10.78        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       20.28        13.87        10.55        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        30.71        59.67        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E5 
       86.40       141.21        48.76        72.26       165.17        68.15 
TCGA-KK-A6E6 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7B1 TCGA-KK-A7B3 
      113.33         6.44        58.36        27.02        34.95        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I8 TCGA-KK-A8IA 
       32.45        74.27       101.79        21.96        31.79        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8IJ 
        2.73        67.43        69.27        82.36        66.18        51.25 
TCGA-KK-A8IK TCGA-M7-A71Y TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A725 TCGA-QU-A6IP 
       67.46         5.19        12.62        13.15        18.84        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8ML 
       18.12         0.89        47.64        28.18        58.88        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       61.68        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        6.64         8.84        25.51        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       44.91        25.78       119.38       109.58       102.90        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       89.49        55.56        60.92        66.97        21.80        58.32 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A9DI TCGA-XJ-A9DK 
       42.94        14.76        12.36        38.04        48.03         9.04 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        75.75        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI 
       32.45       114.38        77.79        68.48         8.98        53.36 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         1.64        14.53        13.28        10.13 

  MLL3 MUTATED MLL3 WILD-TYPE 
         14.04           0.72 
  MLL3 MUTATED MLL3 WILD-TYPE 
        113.98         165.17 
  MLL3 MUTATED MLL3 WILD-TYPE 
         32.91          28.77 
[1] "14.0 - 114.0 (32.9)" "0.7 - 165.2 (28.8)" 
[1] "hr=" "5.3"
D22V2, continuous
                vv
clus              T2  T3  T4
  MLL3 MUTATED     5   8   0
  MLL3 WILD-TYPE 123 186   6
D22V3, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T2            5            123
  T3            8            186
  T4            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V4, binary
                cls
clus               0   1
  MLL3 MUTATED    11   2
  MLL3 WILD-TYPE 222  50
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     11    2
  MLL3 WILD-TYPE  222   50
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           11            222
  1            2             50
[1] 2 2
[1] FALSE
D22V5, binary
                cls
clus               0   1
  MLL3 MUTATED     8   3
  MLL3 WILD-TYPE 244  33
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      8    3
  MLL3 WILD-TYPE  244   33
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO             8            244
  YES            3             33
[1] 2 2
[1] FALSE
D22V6, binary
                cls
clus               0   1
  MLL3 MUTATED     1  12
  MLL3 WILD-TYPE   9 310
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      1   12
  MLL3 WILD-TYPE    9  310
                                        clus
vv                                       MLL3 MUTATED MLL3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1              9
  PROSTATE ADENOCARCINOMA ACINAR TYPE              12            310
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED     9   3   0   1
  MLL3 WILD-TYPE 212  82   4   8
D22V7, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0            9            212
  R1            3             82
  R2            0              4
  RX            1              8
[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"
D22V8, continuous
D22V9, continuous
D22V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED       0                         0     5
  MLL3 WILD-TYPE     2                         7   128
D22V11, multiclass
                           clus
vv                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                5            128
[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"
