[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/22506989/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/22592901/transformed.cor.cli.txt"

nPatients in clinical file=499, in cluster file=498, common to both=498
[1] "Reduce the number of clustering variables from 45 to 44."
[1]  44 498
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            57            441 
  SPOP MUTATED SPOP WILD-TYPE 
            57            441 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            57            441 
  TP53 MUTATED TP53 WILD-TYPE 
            57            441 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            17            481 
  PTEN MUTATED PTEN WILD-TYPE 
            17            481 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
              11              487 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
              11              487 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            469 
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            469 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              13              485 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              13              485 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              484 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              484 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             485 
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             485 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             28             470 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             28             470 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            469 
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            469 
[1] "GAGE2A MUTATION ANALYSIS"
[1] 3
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              493 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              493 
[1] "TNRC18 MUTATION ANALYSIS"
[1] 3
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               9              489 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               9              489 
[1] "AGAP6 MUTATION ANALYSIS"
[1] 3
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             493 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             493 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             6            492 
  IDH1 MUTATED IDH1 WILD-TYPE 
             6            492 
[1] "GATA6 MUTATION ANALYSIS"
[1] 3
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             494 
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             494 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
             8            490 
  SMG7 MUTATED SMG7 WILD-TYPE 
             8            490 
[1] "CNTNAP1 MUTATION ANALYSIS"
[1] 3
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                9               489 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                9               489 
[1] "CDKN1B MUTATION ANALYSIS"
[1] 3
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               6              492 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               6              492 
[1] "EOMES MUTATION ANALYSIS"
[1] 3
  EOMES MUTATED EOMES WILD-TYPE 
              5             493 
  EOMES MUTATED EOMES WILD-TYPE 
              5             493 
[1] "NBPF1 MUTATION ANALYSIS"
[1] 3
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              9             489 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              9             489 
[1] "LMOD2 MUTATION ANALYSIS"
[1] 3
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              6             492 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              6             492 
[1] "EHHADH MUTATION ANALYSIS"
[1] 3
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              493 
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              493 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
              8             490 
  MED12 MUTATED MED12 WILD-TYPE 
              8             490 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              493 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              493 
[1] "TCEB3 MUTATION ANALYSIS"
[1] 3
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             494 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             494 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
              7             491 
  MED15 MUTATED MED15 WILD-TYPE 
              7             491 
[1] "ERF MUTATION ANALYSIS"
[1] 3
  ERF MUTATED ERF WILD-TYPE 
            5           493 
  ERF MUTATED ERF WILD-TYPE 
            5           493 
[1] "ERN1 MUTATION ANALYSIS"
[1] 3
  ERN1 MUTATED ERN1 WILD-TYPE 
             4            494 
  ERN1 MUTATED ERN1 WILD-TYPE 
             4            494 
[1] "MLLT10 MUTATION ANALYSIS"
[1] 3
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               5              493 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               5              493 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             16             482 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             16             482 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             12             486 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             12             486 
[1] "FMN1 MUTATION ANALYSIS"
[1] 3
  FMN1 MUTATED FMN1 WILD-TYPE 
             4            494 
  FMN1 MUTATED FMN1 WILD-TYPE 
             4            494 
[1] "AKT1 MUTATION ANALYSIS"
[1] 3
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            495 
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            495 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           22           476 
  ATM MUTATED ATM WILD-TYPE 
           22           476 
[1] "STRC MUTATION ANALYSIS"
[1] 3
  STRC MUTATED STRC WILD-TYPE 
             5            493 
  STRC MUTATED STRC WILD-TYPE 
             5            493 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           10           488 
  APC MUTATED APC WILD-TYPE 
           10           488 
[1] "ZFP36L2 MUTATION ANALYSIS"
[1] 3
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                4               494 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                4               494 
[1] "MYOT MUTATION ANALYSIS"
[1] 3
  MYOT MUTATED MYOT WILD-TYPE 
             5            493 
  MYOT MUTATED MYOT WILD-TYPE 
             5            493 
[1] "KIRREL MUTATION ANALYSIS"
[1] 3
  KIRREL MUTATED KIRREL WILD-TYPE 
               6              492 
  KIRREL MUTATED KIRREL WILD-TYPE 
               6              492 
[1] "PGBD2 MUTATION ANALYSIS"
[1] 3
  PGBD2 MUTATED PGBD2 WILD-TYPE 
              3             495 
  PGBD2 MUTATED PGBD2 WILD-TYPE 
              3             495 
[1] "LOC100132247 MUTATION ANALYSIS"
[1] 3
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                     3                    495 
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                     3                    495 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            494 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            494 
[1] "CDH16 MUTATION ANALYSIS"
[1] 3
  CDH16 MUTATED CDH16 WILD-TYPE 
              4             494 
  CDH16 MUTATED CDH16 WILD-TYPE 
              4             494 
[1] "KRT25 MUTATION ANALYSIS"
[1] 3
  KRT25 MUTATED KRT25 WILD-TYPE 
              6             492 
  KRT25 MUTATED KRT25 WILD-TYPE 
              6             492 
[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 498 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=10,	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=432,	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=13,	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=11,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'PSA_VALUE':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'DAYS_TO_PSA':	nDistinctValues=383,	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 498 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=36, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
188 293  10 
[1] "table(vv)"
vv
 T2  T3  T4 
188 293  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
188 293  10 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
188 293  10 
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=11, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=94, 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    56   1
  SPOP WILD-TYPE 432   9
  SPOP MUTATED SPOP WILD-TYPE 
            57            441 
  SPOP MUTATED SPOP WILD-TYPE 
             1              9 
$`SPOP MUTATED`
TCGA-EJ-7123 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-CH-5788 TCGA-EJ-5505 TCGA-EJ-5509 
       84.56        41.00        41.49        26.99        30.31        48.13 
TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-8468 TCGA-EJ-A65E 
       41.85        88.34         6.28        38.37        77.16        13.71 
TCGA-EJ-A65M TCGA-EJ-A8FS TCGA-FC-7961 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6369 
        7.56         8.75        15.42        81.04        66.67        39.95 
TCGA-G9-7510 TCGA-HC-7080 TCGA-HC-8258 TCGA-HC-8261 TCGA-HC-A6AP TCGA-J4-A6G3 
       38.96        36.36        27.85        17.95         2.33        27.91 
TCGA-J4-A83J TCGA-J9-A52D TCGA-KC-A7F5 TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 
       22.88         6.97         2.99        83.34        86.40        48.76 
TCGA-KK-A7AQ TCGA-KK-A7B0 TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8IK TCGA-TP-A8TV 
       52.93        43.69        32.91        26.43        67.46        20.05 
TCGA-V1-A9OF TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9ZK TCGA-VN-A88O TCGA-VN-A88R 
       38.93        37.28        35.08        45.47        15.81        25.78 
TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87H TCGA-X4-A8KS TCGA-XJ-A83G TCGA-XK-AAIW 
      102.90        89.49        21.80        32.19        48.03        40.04 
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 TCGA-ZG-A9L6 TCGA-ZG-A9ND 
       13.28        22.59        13.48 

$`SPOP WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       49.74        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
       29.56        32.45         2.73        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 
        1.02        12.99        13.97         1.97         2.99        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        35.01        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       13.02         9.99         2.99        29.00        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-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 
       45.73        46.92        45.40        47.90        64.60        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-7125 TCGA-EJ-7218 
       62.76        58.45        60.23        60.10        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-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D 
       32.32        76.41        38.10        24.85        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       18.41        21.90        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-A4JI 
        9.83         4.54         4.31         4.77        28.41        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        41.62        87.35 
TCGA-G9-6336 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       67.99        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 
       45.30        44.81        64.01        40.18        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        52.93        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       65.26        38.93        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       30.38        22.55        22.32         1.58        15.88        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
       17.42         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
        6.02        25.28        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A5A1 TCGA-KK-A6DY 
        8.88        11.57       113.10        64.70        81.17       141.21 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       90.74        58.19        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       49.94        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG 
       65.82        31.79        63.48        67.43        69.27        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        62.96        16.21 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12         0.89        17.29        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       94.36        20.91        79.00        62.89        12.20        15.65 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZR 
       28.73        27.19        17.75        49.87        53.92        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P 
        8.84        25.51        24.53         6.21        25.18        41.42 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 
       44.91        16.31       119.38        75.91       109.58        23.93 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N 
       55.56        60.92        66.97        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI 
       14.76        45.47        12.36        37.05        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        37.25        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       17.29         4.87        52.96        49.02        51.45        75.75 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SI 
       60.56        16.83        56.52        41.46        45.14        53.06 
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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       36.10         3.09        10.13         4.27        11.67        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       37.94        36.43        29.85        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       14.96        11.47         4.34 

  SPOP MUTATED SPOP WILD-TYPE 
          2.33           0.76 
  SPOP MUTATED SPOP WILD-TYPE 
        114.38         165.17 
  SPOP MUTATED SPOP WILD-TYPE 
         36.36          29.85 
[1] "2.3 - 114.4 (36.4)" "0.8 - 165.2 (29.9)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus              T2  T3  T4
  SPOP MUTATED    26  31   0
  SPOP WILD-TYPE 162 262  10
D1V3, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  T2           26            162
  T3           31            262
  T4            0             10
[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    46   5
  SPOP WILD-TYPE 300  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     46    5
  SPOP WILD-TYPE  300   74
   clus
vv  SPOP MUTATED SPOP WILD-TYPE
  0           46            300
  1            5             74
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  SPOP MUTATED    47   7
  SPOP WILD-TYPE 348  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     47    7
  SPOP WILD-TYPE  348   52
     clus
vv    SPOP MUTATED SPOP WILD-TYPE
  NO            47            348
  YES            7             52
[1] 2 2
[1] FALSE
D1V6, binary
                cls
clus               0   1
  SPOP MUTATED    55   2
  SPOP WILD-TYPE 428  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     55    2
  SPOP WILD-TYPE  428   13
                                        clus
vv                                       SPOP MUTATED SPOP WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              55            428
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            2             13
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    35  13   1   4
  SPOP WILD-TYPE 281 134   4  11
D1V7, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           35            281
  R1           13            134
  R2            1              4
  RX            4             11
[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    12
  SPOP WILD-TYPE     2                         6   135
D1V11, multiclass
                           clus
vv                          SPOP MUTATED SPOP WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                               12            135
[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    54   3
  TP53 WILD-TYPE 434   7
  TP53 MUTATED TP53 WILD-TYPE 
            57            441 
  TP53 MUTATED TP53 WILD-TYPE 
             3              7 
$`TP53 MUTATED`
TCGA-KC-A7FA TCGA-KK-A7B4 TCGA-2A-A8VT TCGA-CH-5761 TCGA-EJ-5507 TCGA-EJ-5514 
       19.66        32.45        45.14         0.92        47.90        60.13 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-8472 TCGA-EJ-A7NH 
       74.93        36.66        33.14        35.28        24.85        15.58 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-HC-7213 
       50.73        38.96        30.97        26.01        29.79        40.08 
TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-8216 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 
       32.91        30.84        22.42        22.36         1.78         2.01 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7171 TCGA-J4-A67L TCGA-J9-A52B TCGA-J9-A8CK 
       19.30        27.75        43.69        25.32        13.87        10.55 
TCGA-KC-A4BL TCGA-KC-A7F6 TCGA-KK-A6DY TCGA-KK-A7AU TCGA-KK-A8IG TCGA-KK-A8II 
       30.71         8.65       141.21        58.36        82.36       113.98 
TCGA-V1-A8MJ TCGA-V1-A9O5 TCGA-V1-A9ZI TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A87D 
       58.88        63.52        53.92       119.38       109.58        60.92 
TCGA-XJ-A9DI TCGA-XK-AAIW TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SB TCGA-YL-A8SJ 
       48.03        40.04        49.02        51.45        56.52        45.86 
TCGA-YL-A9WH TCGA-YL-A9WK TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.04        70.22        49.91        36.10        11.67        42.81 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9M4 
       19.17        12.43        17.98 

$`TP53 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7AP 
       31.43         3.48         7.00        32.61        40.67         6.44 
TCGA-KK-A7B3 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       29.56         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       55.92        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 
        1.02        12.99        13.97         1.97         2.99        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 
        1.02        13.02        35.01        31.00         2.04        44.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        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-5508 TCGA-EJ-5509 
       45.73        46.92        30.31        45.40        64.60        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       62.04        48.53        56.98        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       69.63        64.50        68.35        61.87        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        93.70        83.57 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 
       37.81        25.35        33.83        27.09        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        24.39        38.37        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        45.90         3.75        42.94 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8474 TCGA-EJ-A46D 
       32.32        77.16        76.41        38.10        25.18        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       14.20         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 
       58.22        56.75        64.18        52.93        27.91        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       28.18        32.68        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7231 TCGA-HC-7232 
       14.47        28.54        40.14        28.60        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 
       36.26        35.84        31.69        23.57        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       17.85        24.56        19.36        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
       15.55         0.76         2.20         1.61        17.42         2.33 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 TCGA-J4-8200 
       18.84       109.25        88.24        82.92        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       33.01        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       27.12         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        2.99         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40        81.17        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       32.91        63.48        67.43        69.27        26.43        66.18 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK 
        0.89        17.29        20.05        47.64        28.18        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       22.55        35.44         6.64        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZK 
       35.08        28.73        27.19        17.75        49.87        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A875 
       15.81        41.42        44.91        25.78        16.31        75.91 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
      102.90        23.93        89.49        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       12.36        37.05        48.03        42.08         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
        4.87        52.96        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SK 
       16.83        41.46        45.14        28.77        53.06        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-YL-A9WL TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        24.33         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
        4.27        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9MC 
        3.78        16.96        19.04        12.16        22.75        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  TP53 MUTATED TP53 WILD-TYPE 
          0.92           0.76 
  TP53 MUTATED TP53 WILD-TYPE 
        141.21         165.17 
  TP53 MUTATED TP53 WILD-TYPE 
         36.10          29.23 
[1] "0.9 - 141.2 (36.1)" "0.8 - 165.2 (29.2)"
[1] "hr=" "2.1"
D2V2, continuous
                vv
clus              T2  T3  T4
  TP53 MUTATED    11  44   2
  TP53 WILD-TYPE 177 249   8
D2V3, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T2           11            177
  T3           44            249
  T4            2              8
[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    37  19
  TP53 WILD-TYPE 309  60
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     37   19
  TP53 WILD-TYPE  309   60
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           37            309
  1           19             60
[1] 2 2
[1] FALSE
D2V5, binary
                cls
clus               0   1
  TP53 MUTATED    43  10
  TP53 WILD-TYPE 352  49
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     43   10
  TP53 WILD-TYPE  352   49
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  NO            43            352
  YES           10             49
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  TP53 MUTATED    55   2
  TP53 WILD-TYPE 428  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     55    2
  TP53 WILD-TYPE  428   13
                                        clus
vv                                       TP53 MUTATED TP53 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              55            428
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            2             13
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    29  28   0   0
  TP53 WILD-TYPE 287 119   5  15
D2V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           29            287
  R1           28            119
  R2            0              5
  RX            0             15
[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    12
  TP53 WILD-TYPE     2                         7   135
D2V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                               12            135
[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 = PTEN MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    17   0
  PTEN WILD-TYPE 471  10
  PTEN MUTATED PTEN WILD-TYPE 
            17            481 
  PTEN MUTATED PTEN WILD-TYPE 
             0             10 
$`PTEN MUTATED`
TCGA-CH-5791 TCGA-EJ-7791 TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5740 TCGA-EJ-A65D 
       33.01        36.76        11.51         2.99         1.02        12.92 
TCGA-FC-7961 TCGA-G9-6366 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-A6AL TCGA-KC-A4BV 
       15.42        64.01        28.60        32.91         2.20        43.66 
TCGA-KK-A6E1 TCGA-KK-A6E7 TCGA-KK-A8I6 TCGA-V1-A9Z9 TCGA-ZG-A9L2 
       72.26        90.74        21.96        17.75        37.94 

$`PTEN WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-A46B TCGA-EJ-A46G TCGA-EJ-A65J 
       84.56        36.13        35.18        21.60        21.96        14.83 
TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       28.70        39.39        44.55        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 
       44.84        41.82        20.22         6.97        22.06        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 
       35.01        31.00         2.04         0.92        44.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 
        1.02        15.06        24.03         2.04        13.02        26.99 
TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
        9.99         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        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E 
       17.23        25.74        23.80        21.96        23.34        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7213 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       40.08        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         1.78         2.01         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         2.99         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 
      165.17        67.59       115.13        68.15       113.33        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 
       43.69        34.95        36.13        74.27       101.79        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       28.73        27.19        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
        4.27        11.67        42.81        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  PTEN MUTATED PTEN WILD-TYPE 
          1.02           0.76 
  PTEN MUTATED PTEN WILD-TYPE 
         90.74         165.17 
  PTEN MUTATED PTEN WILD-TYPE 
         28.60          30.51 
[1] "1.0 - 90.7 (28.6)"  "0.8 - 165.2 (30.5)"
[1] "hr="     "2.5e+07"
D3V2, continuous
                vv
clus              T2  T3  T4
  PTEN MUTATED     7  10   0
  PTEN WILD-TYPE 181 283  10
D3V3, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T2            7            181
  T3           10            283
  T4            0             10
[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
  PTEN MUTATED    14   2
  PTEN WILD-TYPE 332  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     14    2
  PTEN WILD-TYPE  332   77
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           14            332
  1            2             77
[1] 2 2
[1] FALSE
D3V5, binary
                cls
clus               0   1
  PTEN MUTATED    11   1
  PTEN WILD-TYPE 384  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     11    1
  PTEN WILD-TYPE  384   58
     clus
vv    PTEN MUTATED PTEN WILD-TYPE
  NO            11            384
  YES            1             58
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus               0   1
  PTEN MUTATED    16   1
  PTEN WILD-TYPE 467  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     16    1
  PTEN WILD-TYPE  467   14
                                        clus
vv                                       PTEN MUTATED PTEN WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              16            467
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            1             14
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED    10   4   0   1
  PTEN WILD-TYPE 306 143   5  14
D3V7, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0           10            306
  R1            4            143
  R2            0              5
  RX            1             14
[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
  PTEN MUTATED       0                         0     8
  PTEN WILD-TYPE     2                         7   139
D3V11, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                8            139
[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 = NUDT11 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED    11   0
  NUDT11 WILD-TYPE 477  10
  NUDT11 MUTATED NUDT11 WILD-TYPE 
              11              487 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               0               10 
$`NUDT11 MUTATED`
TCGA-CH-5791 TCGA-EJ-5519 TCGA-EJ-A46E TCGA-EJ-A7NG TCGA-G9-6333 TCGA-M7-A71Z 
       33.01        64.50        17.23        14.20        81.04        21.14 
TCGA-V1-A9OT TCGA-YL-A8HM TCGA-YL-A8SQ TCGA-ZG-A8QZ TCGA-ZG-A9MC 
       15.65        48.72        68.48        10.13        14.96 

$`NUDT11 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-EJ-5542 
        1.02        12.00         1.02        15.98        32.02        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       74.93        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       24.85        25.18        20.58        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
       11.61         8.22        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 
       17.23        25.94        20.25        41.62        87.35        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.44        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       26.01        29.79        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87        27.85        30.38        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        15.55        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         2.99         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        83.34        64.70        86.40        81.17       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        58.19        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        25.18        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       17.29         4.87        52.96        49.02        51.45        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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       77.79         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        17.98        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
           10.13             0.76 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           81.04           165.17 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           21.14            30.51 
[1] "10.1 - 81.0 (21.1)" "0.8 - 165.2 (30.5)"
[1] "hr="     "9200000"
D4V2, continuous
                  vv
clus                T2  T3  T4
  NUDT11 MUTATED     2   8   0
  NUDT11 WILD-TYPE 186 285  10
D4V3, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T2              2              186
  T3              8              285
  T4              0               10
[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
  NUDT11 MUTATED     7   3
  NUDT11 WILD-TYPE 339  76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      7    3
  NUDT11 WILD-TYPE  339   76
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              7              339
  1              3               76
[1] 2 2
[1] FALSE
D4V5, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     8   3
  NUDT11 WILD-TYPE 387  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      8    3
  NUDT11 WILD-TYPE  387   56
     clus
vv    NUDT11 MUTATED NUDT11 WILD-TYPE
  NO               8              387
  YES              3               56
[1] 2 2
[1] FALSE
D4V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED    11   0
  NUDT11 WILD-TYPE 472  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED     11    0
  NUDT11 WILD-TYPE  472   15
                                        clus
vv                                       NUDT11 MUTATED NUDT11 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                11              472
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NUDT11 MUTATED     6   5   0   0
  NUDT11 WILD-TYPE 310 142   5  15
D4V7, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  R0              6              310
  R1              5              142
  R2              0                5
  RX              0               15
[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
  NUDT11 MUTATED       0                         0     3
  NUDT11 WILD-TYPE     2                         7   144
D4V11, multiclass
                           clus
vv                          NUDT11 MUTATED NUDT11 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[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 = MLL2 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MLL2 MUTATED    29   0
  MLL2 WILD-TYPE 459  10
  MLL2 MUTATED MLL2 WILD-TYPE 
            29            469 
  MLL2 MUTATED MLL2 WILD-TYPE 
             0             10 
$`MLL2 MUTATED`
TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A8IB TCGA-CH-5752 TCGA-EJ-5495 TCGA-EJ-5531 
       19.66         6.44         2.73        31.00        57.86        41.85 
TCGA-EJ-8468 TCGA-EJ-A8FN TCGA-HC-7738 TCGA-HC-8216 TCGA-HI-7170 TCGA-J4-AAU2 
       77.16        10.82        31.69        22.42        82.92        27.12 
TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A6E3 TCGA-KK-A6E5 TCGA-V1-A8MM TCGA-V1-A9ZI 
        5.85       113.10        67.59        68.15        39.29        53.92 
TCGA-V1-A9ZK TCGA-VN-A88P TCGA-X4-A8KQ TCGA-XK-AAIW TCGA-YJ-A8SW TCGA-YL-A8SB 
       45.47        41.42        45.47        40.04         4.87        56.52 
TCGA-YL-A8SI TCGA-YL-A8SQ TCGA-ZG-A9L0 TCGA-ZG-A9L5 TCGA-ZG-A9MC 
       53.06        68.48        11.67        29.85        14.96 

$`MLL2 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KK-A7B3 
       31.43         3.48         7.00        32.61        40.67        29.56 
TCGA-KK-A7B4 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
       32.45        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 
        1.02        12.99        13.97         1.97         2.99        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
        1.02        13.02        35.01         2.04         0.92        44.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       26.99         9.99         2.99        29.00        48.56        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-5532 TCGA-EJ-7115 
       36.66        62.76        58.45        60.23        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 
       36.33        45.90         3.75        42.94        32.32        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21         6.48         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       35.84        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       88.24        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J9-A52B 
       10.78        23.67        17.85        18.18        13.55        13.87 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        6.97        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        2.99         8.65         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E4 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
      115.13       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU TCGA-V1-A8WL 
       28.18        58.88        16.70        14.73        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       17.75        49.87        44.75         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
        6.21        25.18        15.81        44.91        25.78        16.31 
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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       44.88        14.76        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK 
        4.80        25.32        32.61        17.29        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-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-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        77.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        42.81        37.94        36.43 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       19.04        12.16        22.75        17.98        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  MLL2 MUTATED MLL2 WILD-TYPE 
          2.73           0.76 
  MLL2 MUTATED MLL2 WILD-TYPE 
        113.10         165.17 
  MLL2 MUTATED MLL2 WILD-TYPE 
         40.04          30.31 
[1] "2.7 - 113.1 (40.0)" "0.8 - 165.2 (30.3)"
[1] "hr="     "2.7e+07"
D5V2, continuous
                vv
clus              T2  T3  T4
  MLL2 MUTATED     6  22   1
  MLL2 WILD-TYPE 182 271   9
D5V3, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  T2            6            182
  T3           22            271
  T4            1              9
[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
  MLL2 MUTATED    22   5
  MLL2 WILD-TYPE 324  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     22    5
  MLL2 WILD-TYPE  324   74
   clus
vv  MLL2 MUTATED MLL2 WILD-TYPE
  0           22            324
  1            5             74
[1] 2 2
[1] FALSE
D5V5, binary
                cls
clus               0   1
  MLL2 MUTATED    22   4
  MLL2 WILD-TYPE 373  55
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     22    4
  MLL2 WILD-TYPE  373   55
     clus
vv    MLL2 MUTATED MLL2 WILD-TYPE
  NO            22            373
  YES            4             55
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus               0   1
  MLL2 MUTATED    28   1
  MLL2 WILD-TYPE 455  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED     28    1
  MLL2 WILD-TYPE  455   14
                                        clus
vv                                       MLL2 MUTATED MLL2 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              28            455
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            1             14
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL2 MUTATED    20   8   0   1
  MLL2 WILD-TYPE 296 139   5  14
D5V7, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  R0           20            296
  R1            8            139
  R2            0              5
  RX            1             14
[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
  MLL2 MUTATED       0                         0     5
  MLL2 WILD-TYPE     2                         7   142
D5V11, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                5            142
[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 = CTNNB1 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    13   0
  CTNNB1 WILD-TYPE 475  10
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              13              485 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               0               10 
$`CTNNB1 MUTATED`
TCGA-QU-A6IM TCGA-CH-5752 TCGA-EJ-5494 TCGA-EJ-5525 TCGA-EJ-A65D TCGA-HC-7212 
       41.00        31.00        48.56        36.66        12.92        28.60 
TCGA-HC-7738 TCGA-HC-8262 TCGA-KK-A6DY TCGA-M7-A722 TCGA-VP-A87H TCGA-XK-AAIW 
       31.69        22.32       141.21        34.85        21.80        40.04 
TCGA-ZG-A9LB 
       19.17 

$`CTNNB1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56        32.45         2.73        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5754 
        2.99        24.03         1.02        13.02        35.01         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         2.99        29.00 
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        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        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-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.44        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       26.01        29.79        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        40.14        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       38.17        36.26        35.84        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 
       23.87        27.85        30.38        22.55        17.95         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40        81.17        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 
       62.96        16.21        21.14        12.62        13.15        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        58.32        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        37.25        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           12.92             0.76 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          141.21           165.17 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           31.69            30.38 
[1] "12.9 - 141.2 (31.7)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "2.9e+07"
D6V2, continuous
                  vv
clus                T2  T3  T4
  CTNNB1 MUTATED     6   7   0
  CTNNB1 WILD-TYPE 182 286  10
D6V3, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T2              6              182
  T3              7              286
  T4              0               10
[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
  CTNNB1 MUTATED    12   0
  CTNNB1 WILD-TYPE 334  79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     12    0
  CTNNB1 WILD-TYPE  334   79
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             12              334
  1              0               79
[1] 2 2
[1] FALSE
D6V5, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    11   1
  CTNNB1 WILD-TYPE 384  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     11    1
  CTNNB1 WILD-TYPE  384   58
     clus
vv    CTNNB1 MUTATED CTNNB1 WILD-TYPE
  NO              11              384
  YES              1               58
[1] 2 2
[1] FALSE
D6V6, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    12   1
  CTNNB1 WILD-TYPE 471  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     12    1
  CTNNB1 WILD-TYPE  471   14
                                        clus
vv                                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                12              471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              1               14
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED     7   4   1   0
  CTNNB1 WILD-TYPE 309 143   4  15
D6V7, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              7              309
  R1              4              143
  R2              1                4
  RX              0               15
[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
  CTNNB1 MUTATED       0                         0     5
  CTNNB1 WILD-TYPE     2                         7   142
D6V11, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[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 = PIK3CA MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    14   0
  PIK3CA WILD-TYPE 474  10
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              484 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0               10 
$`PIK3CA MUTATED`
TCGA-XK-AAJ3 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-8469 TCGA-EJ-A65D TCGA-HC-7078 
       41.49        36.66        62.76        76.41        12.92        65.26 
TCGA-HC-7081 TCGA-HC-7231 TCGA-HC-A6AN TCGA-HC-A9TH TCGA-J9-A8CL TCGA-QU-A6IN 
       37.35        30.87         1.61        27.75        13.32       140.19 
TCGA-VP-A87H TCGA-XK-AAIW 
       21.80        40.04 

$`PIK3CA WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAK1 
        6.44        29.56        32.45         2.73        41.00        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5527 TCGA-EJ-5530 
       64.50        74.93        68.35        61.87        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        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-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-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       42.94        32.32        77.16        38.10        24.85        25.18 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.44        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       26.01        29.79        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 
       19.76        69.53        38.93        36.36        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7736 
       40.14        28.60        40.08        32.91        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        2.20        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HI-7168 
        4.93         9.53        25.48        18.84        19.30       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       27.12        13.87         5.85         6.97        10.62        10.55 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         2.99         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        83.34        64.70        86.40        81.17       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        90.74        58.19        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        57.67        49.94        43.69        34.95        36.13 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       74.27       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
       63.48        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        67.46        20.65        62.96        16.21 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         5.69         3.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-A87J 
       23.93        89.49        55.56        60.92        66.97        58.32 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            1.61             0.76 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          140.19           165.17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          37.005           30.365 
[1] "1.6 - 140.2 (37.0)" "0.8 - 165.2 (30.4)"
[1] "hr="     "2.8e+07"
D7V2, continuous
                  vv
clus                T2  T3  T4
  PIK3CA MUTATED     3  11   0
  PIK3CA WILD-TYPE 185 282  10
D7V3, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T2              3              185
  T3             11              282
  T4              0               10
[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
  PIK3CA MUTATED    10   1
  PIK3CA WILD-TYPE 336  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    1
  PIK3CA WILD-TYPE  336   78
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             10              336
  1              1               78
[1] 2 2
[1] FALSE
D7V5, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    11   1
  PIK3CA WILD-TYPE 384  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     11    1
  PIK3CA WILD-TYPE  384   58
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO              11              384
  YES              1               58
[1] 2 2
[1] FALSE
D7V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    13   1
  PIK3CA WILD-TYPE 470  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     13    1
  PIK3CA WILD-TYPE  470   14
                                        clus
vv                                       PIK3CA MUTATED PIK3CA WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                13              470
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              1               14
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED     7   4   2   1
  PIK3CA WILD-TYPE 309 143   3  14
D7V7, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0              7              309
  R1              4              143
  R2              2                3
  RX              1               14
[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
  PIK3CA MUTATED       0                         0     5
  PIK3CA WILD-TYPE     2                         7   142
D7V11, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[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 = KDM6A MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED    13   0
  KDM6A WILD-TYPE 475  10
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             485 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0              10 
$`KDM6A MUTATED`
TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-EJ-5509 TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-A65G 
       41.49        32.19        48.13        25.35        24.39        21.90 
TCGA-HC-7212 TCGA-KK-A6E8 TCGA-V1-A8ML TCGA-XA-A8JR TCGA-XK-AAIW TCGA-YL-A9WK 
       28.60        58.19        14.73        12.36        40.04        70.22 
TCGA-ZG-A9M4 
       17.98 

$`KDM6A WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-2A-A8VL 
        6.44        29.56        32.45         2.73        41.00        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
       22.06         1.02        12.99        13.97         1.97         2.99 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         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        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        88.34        93.70        83.57        37.81 
TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.14        33.83        27.09        30.35        27.68         6.28 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       13.71        18.41         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54        40.14        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        6.97        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        2.99         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       64.70        86.40        81.17       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MM 
       20.05        47.64        28.18        58.88        16.70        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        45.47        32.19        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       14.04        53.36        60.99        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        14.96        11.47        13.48         4.34 

  KDM6A MUTATED KDM6A WILD-TYPE 
          12.36            0.76 
  KDM6A MUTATED KDM6A WILD-TYPE 
          70.22          165.17 
  KDM6A MUTATED KDM6A WILD-TYPE 
          28.60           30.51 
[1] "12.4 - 70.2 (28.6)" "0.8 - 165.2 (30.5)"
[1] "hr="     "9200000"
D8V2, continuous
                 vv
clus               T2  T3  T4
  KDM6A MUTATED     9   4   0
  KDM6A WILD-TYPE 179 289  10
D8V3, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T2             9             179
  T3             4             289
  T4             0              10
[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
  KDM6A MUTATED    12   1
  KDM6A WILD-TYPE 334  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     12    1
  KDM6A WILD-TYPE  334   78
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            12             334
  1             1              78
[1] 2 2
[1] FALSE
D8V5, binary
                 cls
clus                0   1
  KDM6A MUTATED    12   0
  KDM6A WILD-TYPE 383  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     12    0
  KDM6A WILD-TYPE  383   59
     clus
vv    KDM6A MUTATED KDM6A WILD-TYPE
  NO             12             383
  YES             0              59
[1] 2 2
[1] FALSE
D8V6, binary
                 cls
clus                0   1
  KDM6A MUTATED    13   0
  KDM6A WILD-TYPE 470  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     13    0
  KDM6A WILD-TYPE  470   15
                                        clus
vv                                       KDM6A MUTATED KDM6A WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               13             470
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED     7   3   1   1
  KDM6A WILD-TYPE 309 144   4  14
D8V7, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0             7             309
  R1             3             144
  R2             1               4
  RX             1              14
[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
  KDM6A MUTATED       0                         0     4
  KDM6A WILD-TYPE     2                         7   143
D8V11, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             143
[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 = FOXA1 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  FOXA1 MUTATED    28   0
  FOXA1 WILD-TYPE 460  10
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             28             470 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              0              10 
$`FOXA1 MUTATED`
TCGA-KK-A8IB TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-EJ-5494 TCGA-EJ-7330 
        2.73        45.30         3.68         2.99        48.56         6.28 
TCGA-EJ-7782 TCGA-EJ-7789 TCGA-G9-6351 TCGA-HC-7210 TCGA-HC-8265 TCGA-HC-A6AO 
       38.37        36.33        67.33        28.54        15.88        17.42 
TCGA-HC-A6AP TCGA-J9-A8CP TCGA-KC-A7F5 TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK 
        2.33        12.69         2.99        26.43        82.36        67.46 
TCGA-M7-A722 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-V1-A8MM TCGA-V1-A9OQ TCGA-VP-AA1N 
       34.85         3.19       140.19        39.29        12.20        44.88 
TCGA-YJ-A8SW TCGA-YL-A8S9 TCGA-YL-A9WI TCGA-ZG-A9LB 
        4.87        60.56        53.36        19.17 

$`FOXA1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
        6.44        29.56        32.45        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-2A-AAYF 
       20.42        55.92        45.14        22.06        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 
       41.82        20.22        11.51         6.97        22.06         1.02 
TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 
       12.99        13.97         1.97         2.99        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         2.04         0.92        44.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 
       26.99         9.99         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-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        93.70        83.57        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
       33.83        27.09        30.35        27.68        24.39        35.28 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7792 
       25.87        25.68        38.70        36.03        28.24        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       80.55        68.68        49.81        50.70        67.92        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        45.30        44.81        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       28.18        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       36.36        37.35        14.47        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AS 
        0.76         1.78         2.01         2.20         1.61         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-KC-A4BL 
        6.97        10.62        10.55        13.32        15.22        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        83.34        64.70        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       81.17       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH 
       31.79        32.91        63.48        67.43        69.27        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
      113.98        51.25        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       12.62        13.15        25.08        29.23        18.84         5.69 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MU 
       47.64        28.18        58.88        16.70        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       62.89        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-X4-A8KQ TCGA-X4-A8KS 
       21.80        58.32        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       32.61        17.29        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       75.75        62.14        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       77.79        68.48         8.98        14.04        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       29.85        22.59        20.28        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  FOXA1 MUTATED FOXA1 WILD-TYPE 
           2.33            0.76 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
         140.19          165.17 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
         27.485          30.545 
[1] "2.3 - 140.2 (27.5)" "0.8 - 165.2 (30.5)"
[1] "hr="     "7.7e+07"
D9V2, continuous
                 vv
clus               T2  T3  T4
  FOXA1 MUTATED    10  18   0
  FOXA1 WILD-TYPE 178 275  10
D9V3, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  T2            10             178
  T3            18             275
  T4             0              10
[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
  FOXA1 MUTATED    22   1
  FOXA1 WILD-TYPE 324  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     22    1
  FOXA1 WILD-TYPE  324   78
   clus
vv  FOXA1 MUTATED FOXA1 WILD-TYPE
  0            22             324
  1             1              78
[1] 2 2
[1] FALSE
D9V5, binary
                 cls
clus                0   1
  FOXA1 MUTATED    18   3
  FOXA1 WILD-TYPE 377  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     18    3
  FOXA1 WILD-TYPE  377   56
     clus
vv    FOXA1 MUTATED FOXA1 WILD-TYPE
  NO             18             377
  YES             3              56
[1] 2 2
[1] FALSE
D9V6, binary
                 cls
clus                0   1
  FOXA1 MUTATED    27   1
  FOXA1 WILD-TYPE 456  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     27    1
  FOXA1 WILD-TYPE  456   14
                                        clus
vv                                       FOXA1 MUTATED FOXA1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               27             456
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             1              14
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXA1 MUTATED    17  10   0   1
  FOXA1 WILD-TYPE 299 137   5  14
D9V7, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  R0            17             299
  R1            10             137
  R2             0               5
  RX             1              14
[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
  FOXA1 MUTATED       0                         2     5
  FOXA1 WILD-TYPE     2                         5   142
D9V11, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               5
  WHITE                                 5             142
[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 = MLL3 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    27   2
  MLL3 WILD-TYPE 461   8
  MLL3 MUTATED MLL3 WILD-TYPE 
            29            469 
  MLL3 MUTATED MLL3 WILD-TYPE 
             2              8 
$`MLL3 MUTATED`
TCGA-EJ-7123 TCGA-HC-7233 TCGA-CH-5752 TCGA-EJ-5519 TCGA-EJ-5524 TCGA-EJ-A7NH 
       84.56        44.55        31.00        64.50        61.87        15.58 
TCGA-G9-6373 TCGA-HC-7817 TCGA-HC-A4ZV TCGA-HI-7170 TCGA-J4-A83L TCGA-J4-AAU2 
       26.66        30.51         0.76        82.92        23.67        27.12 
TCGA-KC-A7FD TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8II 
        8.88       113.10        83.34        32.91        26.43       113.98 
TCGA-KK-A8IL TCGA-V1-A9OT TCGA-V1-A9OX TCGA-VN-A88L TCGA-VP-A875 TCGA-VP-AA1N 
       20.65        15.65        37.28        24.53        75.91        44.88 
TCGA-XK-AAIW TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WL TCGA-ZG-A9KY 
       40.04         8.98        14.04        24.33         4.27 

$`MLL3 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       49.74        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7748 TCGA-HC-7821 TCGA-HC-A6AQ 
       14.83        28.70        39.39        26.04        31.43         3.48 
TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP TCGA-KK-A7B3 
        7.00        32.61        40.67        19.66         6.44        29.56 
TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL 
       32.45         2.73        41.00        41.49        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
       22.06         1.02        12.99        13.97         1.97         2.99 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 
       24.03         1.02        13.02        35.01         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         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-5521 TCGA-EJ-5522 
       60.23        62.10        62.10        69.63        74.93        68.35 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        25.74        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF 
       13.71        18.41        21.90         7.56        11.61         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       14.20         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7818 
       23.70        24.59        23.80        17.16        25.71        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
       15.88        15.55        22.36         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
      109.25        88.24        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J9-A52B 
       22.88        10.78        17.85        18.18        13.55        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
        5.85         6.97        10.62        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FE TCGA-KK-A59Y TCGA-KK-A59Z 
       21.86         2.99         8.65        11.57        64.70        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       81.17       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG TCGA-KK-A8IH 
       31.79        63.48        67.43        69.27        82.36        66.18 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.25        67.46        62.96        16.21        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OY 
       20.91        38.93        79.00        62.89        12.20        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
       44.75         8.84        25.51         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A876 
       41.42        44.91        25.78        16.31       119.38       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-X4-A8KQ TCGA-X4-A8KS 
       21.80        58.32        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        37.25        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
      114.38        77.79        68.48        53.36        60.99        70.22 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  MLL3 MUTATED MLL3 WILD-TYPE 
          0.76           0.89 
  MLL3 MUTATED MLL3 WILD-TYPE 
        113.98         165.17 
  MLL3 MUTATED MLL3 WILD-TYPE 
         30.51          30.38 
[1] "0.8 - 114.0 (30.5)" "0.9 - 165.2 (30.4)"
[1] "hr=" "3.2"
D10V2, continuous
                vv
clus              T2  T3  T4
  MLL3 MUTATED     9  19   1
  MLL3 WILD-TYPE 179 274   9
D10V3, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T2            9            179
  T3           19            274
  T4            1              9
[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
  MLL3 MUTATED    21   5
  MLL3 WILD-TYPE 325  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     21    5
  MLL3 WILD-TYPE  325   74
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           21            325
  1            5             74
[1] 2 2
[1] FALSE
D10V5, binary
                cls
clus               0   1
  MLL3 MUTATED    19   7
  MLL3 WILD-TYPE 376  52
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     19    7
  MLL3 WILD-TYPE  376   52
     clus
vv    MLL3 MUTATED MLL3 WILD-TYPE
  NO            19            376
  YES            7             52
[1] 2 2
[1] FALSE
D10V6, binary
                cls
clus               0   1
  MLL3 MUTATED    28   1
  MLL3 WILD-TYPE 455  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     28    1
  MLL3 WILD-TYPE  455   14
                                        clus
vv                                       MLL3 MUTATED MLL3 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              28            455
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            1             14
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MLL3 MUTATED    17  10   0   1
  MLL3 WILD-TYPE 299 137   5  14
D10V7, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  R0           17            299
  R1           10            137
  R2            0              5
  RX            1             14
[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
  MLL3 MUTATED       0                         0     7
  MLL3 WILD-TYPE     2                         7   140
D10V11, multiclass
                           clus
vv                          MLL3 MUTATED MLL3 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                7            140
[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 = GAGE2A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  GAGE2A MUTATED     5   0
  GAGE2A WILD-TYPE 483  10
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               5              493 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               0               10 
$`GAGE2A MUTATED`
TCGA-EJ-5497 TCGA-G9-6348 TCGA-HC-A9TH TCGA-J4-AATZ TCGA-M7-A720 
       13.32        49.81        27.75        13.55        12.62 

$`GAGE2A WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 
        2.99        29.00        48.56        57.86        19.56        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       55.76        80.55        68.68        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       27.12        13.87         5.85         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       16.21        21.14        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        58.32        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  GAGE2A MUTATED GAGE2A WILD-TYPE 
           12.62             0.76 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           49.81           165.17 
  GAGE2A MUTATED GAGE2A WILD-TYPE 
           13.55            30.58 
[1] "12.6 - 49.8 (13.6)" "0.8 - 165.2 (30.6)"
[1] "hr="     "3300000"
D11V2, continuous
                  vv
clus                T2  T3  T4
  GAGE2A MUTATED     3   2   0
  GAGE2A WILD-TYPE 185 291  10
D11V3, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  T2              3              185
  T3              2              291
  T4              0               10
[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
  GAGE2A MUTATED     4   0
  GAGE2A WILD-TYPE 342  79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      4    0
  GAGE2A WILD-TYPE  342   79
   clus
vv  GAGE2A MUTATED GAGE2A WILD-TYPE
  0              4              342
  1              0               79
[1] 2 2
[1] FALSE
D11V5, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     4   1
  GAGE2A WILD-TYPE 391  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      4    1
  GAGE2A WILD-TYPE  391   58
     clus
vv    GAGE2A MUTATED GAGE2A WILD-TYPE
  NO               4              391
  YES              1               58
[1] 2 2
[1] FALSE
D11V6, binary
                  cls
clus                 0   1
  GAGE2A MUTATED     5   0
  GAGE2A WILD-TYPE 478  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2A MUTATED      5    0
  GAGE2A WILD-TYPE  478   15
                                        clus
vv                                       GAGE2A MUTATED GAGE2A WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GAGE2A MUTATED     3   2   0   0
  GAGE2A WILD-TYPE 313 145   5  15
D11V7, multiclass
    clus
vv   GAGE2A MUTATED GAGE2A WILD-TYPE
  R0              3              313
  R1              2              145
  R2              0                5
  RX              0               15
[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
  GAGE2A MUTATED       0                         0     2
  GAGE2A WILD-TYPE     2                         7   145
D11V11, multiclass
[1] "Remove cluster labels:" "GAGE2A MUTATED"        
clus
  GAGE2A MUTATED GAGE2A WILD-TYPE 
               2              154 
      TCGA-CH-5753       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5772 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-EJ-5542       TCGA-EJ-7123 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7791       TCGA-G9-6364       TCGA-HC-7233       TCGA-HC-7748 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7821       TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5740       TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5745       TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5754       TCGA-CH-5761 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5788 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5498       TCGA-EJ-5499 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504       TCGA-EJ-5505 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508       TCGA-EJ-5509 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512       TCGA-EJ-5514 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517       TCGA-EJ-5518 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522       TCGA-EJ-5524 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527       TCGA-EJ-5530 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-7115       TCGA-EJ-7125 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6365 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369       TCGA-G9-6370 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494       TCGA-G9-6496 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075       TCGA-HC-7077 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080       TCGA-HC-7081 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231       TCGA-HC-7232 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7736       TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7742       TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HI-7168       TCGA-HI-7169 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"GAGE2A WILD-TYPE" "GAGE2A WILD-TYPE" 

Clustering(12) Variable = TNRC18 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  TNRC18 MUTATED     9   0
  TNRC18 WILD-TYPE 479  10
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               9              489 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               0               10 
$`TNRC18 MUTATED`
TCGA-XK-AAJ3 TCGA-EJ-7330 TCGA-HC-7742 TCGA-KK-A6E1 TCGA-QU-A6IN TCGA-TK-A8OK 
       41.49         6.28        30.84        72.26       140.19         0.89 
TCGA-V1-A9OA TCGA-XK-AAIW TCGA-XQ-A8TB 
       20.91        40.04        25.32 

$`TNRC18 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAK1 
        6.44        29.56        32.45         2.73        41.00        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       35.84        31.69        23.57        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       13.55        27.12        13.87         5.85         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        83.34        64.70        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       81.17       141.21        48.76       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IO TCGA-QU-A6IP 
       29.23        18.84         5.69         3.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
       18.12        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       94.36        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        25.18        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       47.15        51.81         4.80        32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        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-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  TNRC18 MUTATED TNRC18 WILD-TYPE 
            0.89             0.76 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
          140.19           165.17 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
           30.84            30.38 
[1] "0.9 - 140.2 (30.8)" "0.8 - 165.2 (30.4)"
[1] "hr="     "2.9e+07"
D12V2, continuous
                  vv
clus                T2  T3  T4
  TNRC18 MUTATED     1   7   0
  TNRC18 WILD-TYPE 187 286  10
D12V3, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  T2              1              187
  T3              7              286
  T4              0               10
[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
  TNRC18 MUTATED     6   2
  TNRC18 WILD-TYPE 340  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      6    2
  TNRC18 WILD-TYPE  340   77
   clus
vv  TNRC18 MUTATED TNRC18 WILD-TYPE
  0              6              340
  1              2               77
[1] 2 2
[1] FALSE
D12V5, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     5   3
  TNRC18 WILD-TYPE 390  56
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      5    3
  TNRC18 WILD-TYPE  390   56
     clus
vv    TNRC18 MUTATED TNRC18 WILD-TYPE
  NO               5              390
  YES              3               56
[1] 2 2
[1] FALSE
D12V6, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     9   0
  TNRC18 WILD-TYPE 474  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      9    0
  TNRC18 WILD-TYPE  474   15
                                        clus
vv                                       TNRC18 MUTATED TNRC18 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 9              474
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNRC18 MUTATED     5   2   0   1
  TNRC18 WILD-TYPE 311 145   5  14
D12V7, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  R0              5              311
  R1              2              145
  R2              0                5
  RX              1               14
[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
  TNRC18 MUTATED       0                         0     2
  TNRC18 WILD-TYPE     2                         7   145
D12V11, multiclass
[1] "Remove cluster labels:" "TNRC18 MUTATED"        
clus
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               2              154 
      TCGA-CH-5753       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5772 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-EJ-5542       TCGA-EJ-7123 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7791       TCGA-G9-6364       TCGA-HC-7233       TCGA-HC-7748 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7821       TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5740       TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5745       TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5754       TCGA-CH-5761 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5788 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-7115 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7125       TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7321       TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7331 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7736       TCGA-HC-7737       TCGA-HC-7738 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HI-7168       TCGA-HI-7169 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 

Clustering(13) Variable = AGAP6 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  AGAP6 MUTATED     5   0
  AGAP6 WILD-TYPE 483  10
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              5             493 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              0              10 
$`AGAP6 MUTATED`
TCGA-EJ-A46B TCGA-EJ-5518 TCGA-HC-7747 TCGA-V1-A9Z8 TCGA-VP-A87K 
       21.60        69.63        24.59        27.19        42.94 

$`AGAP6 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46G 
       49.74        84.56        36.13        35.18        36.76        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5519 
       56.98        60.13        60.23        62.10        62.10        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        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       13.55        27.12        13.87         5.85         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        83.34        64.70        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       81.17       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ 
      115.13        68.15       113.33        90.74        58.19        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        57.67        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       28.73        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        58.32        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  AGAP6 MUTATED AGAP6 WILD-TYPE 
          21.60            0.76 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          69.63          165.17 
  AGAP6 MUTATED AGAP6 WILD-TYPE 
          27.19           30.51 
[1] "21.6 - 69.6 (27.2)" "0.8 - 165.2 (30.5)"
[1] "hr="     "3300000"
D13V2, continuous
                 vv
clus               T2  T3  T4
  AGAP6 MUTATED     1   3   1
  AGAP6 WILD-TYPE 187 290   9
D13V3, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  T2             1             187
  T3             3             290
  T4             1               9
[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
  AGAP6 MUTATED     5   0
  AGAP6 WILD-TYPE 341  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      5    0
  AGAP6 WILD-TYPE  341   79
   clus
vv  AGAP6 MUTATED AGAP6 WILD-TYPE
  0             5             341
  1             0              79
[1] 2 2
[1] FALSE
D13V5, binary
                 cls
clus                0   1
  AGAP6 MUTATED     4   1
  AGAP6 WILD-TYPE 391  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    1
  AGAP6 WILD-TYPE  391   58
     clus
vv    AGAP6 MUTATED AGAP6 WILD-TYPE
  NO              4             391
  YES             1              58
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus                0   1
  AGAP6 MUTATED     4   1
  AGAP6 WILD-TYPE 479  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AGAP6 MUTATED      4    1
  AGAP6 WILD-TYPE  479   14
                                        clus
vv                                       AGAP6 MUTATED AGAP6 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             1              14
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AGAP6 MUTATED     1   3   0   0
  AGAP6 WILD-TYPE 315 144   5  15
D13V7, multiclass
    clus
vv   AGAP6 MUTATED AGAP6 WILD-TYPE
  R0             1             315
  R1             3             144
  R2             0               5
  RX             0              15
[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
  AGAP6 MUTATED       0                         0     2
  AGAP6 WILD-TYPE     2                         7   145
D13V11, multiclass
[1] "Remove cluster labels:" "AGAP6 MUTATED"         
clus
  AGAP6 MUTATED AGAP6 WILD-TYPE 
              2             154 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115      TCGA-EJ-7125 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168      TCGA-HI-7169 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"AGAP6 WILD-TYPE" "AGAP6 WILD-TYPE" 

Clustering(14) Variable = IDH1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     6   0
  IDH1 WILD-TYPE 482  10
  IDH1 MUTATED IDH1 WILD-TYPE 
             6            492 
  IDH1 MUTATED IDH1 WILD-TYPE 
             0             10 
$`IDH1 MUTATED`
TCGA-CH-5772 TCGA-EJ-7125 TCGA-G9-7523 TCGA-KK-A6E7 TCGA-M7-A722 TCGA-XK-AAIW 
       15.98        93.70        28.18        90.74        34.85        40.04 

$`IDH1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7218 
       58.45        60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       13.55        27.12        13.87         5.85         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        83.34        64.70        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       81.17       141.21        48.76        72.26       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
      115.13        68.15       113.33        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 
       16.21        21.14        12.62        13.15        25.08        29.23 
TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         5.69         3.19       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        58.32        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        37.25        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  IDH1 MUTATED IDH1 WILD-TYPE 
         15.98           0.76 
  IDH1 MUTATED IDH1 WILD-TYPE 
         93.70         165.17 
  IDH1 MUTATED IDH1 WILD-TYPE 
        37.445         30.380 
[1] "16.0 - 93.7 (37.4)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9400000"
D14V2, continuous
                vv
clus              T2  T3  T4
  IDH1 MUTATED     1   5   0
  IDH1 WILD-TYPE 187 288  10
D14V3, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T2            1            187
  T3            5            288
  T4            0             10
[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
  IDH1 MUTATED     5   1
  IDH1 WILD-TYPE 341  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      5    1
  IDH1 WILD-TYPE  341   78
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            5            341
  1            1             78
[1] 2 2
[1] FALSE
D14V5, binary
                cls
clus               0   1
  IDH1 MUTATED     5   1
  IDH1 WILD-TYPE 390  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      5    1
  IDH1 WILD-TYPE  390   58
     clus
vv    IDH1 MUTATED IDH1 WILD-TYPE
  NO             5            390
  YES            1             58
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus               0   1
  IDH1 MUTATED     6   0
  IDH1 WILD-TYPE 477  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      6    0
  IDH1 WILD-TYPE  477   15
                                        clus
vv                                       IDH1 MUTATED IDH1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               6            477
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED     1   5   0   0
  IDH1 WILD-TYPE 315 142   5  15
D14V7, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0            1            315
  R1            5            142
  R2            0              5
  RX            0             15
[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
  IDH1 MUTATED       0                         0     2
  IDH1 WILD-TYPE     2                         7   145
D14V11, multiclass
[1] "Remove cluster labels:" "IDH1 MUTATED"          
clus
  IDH1 MUTATED IDH1 WILD-TYPE 
             2            154 
    TCGA-CH-5753     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5790 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-EJ-5542     TCGA-EJ-7123     TCGA-EJ-7791 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6364     TCGA-HC-7233     TCGA-HC-7748     TCGA-HC-7821 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5788     TCGA-CH-5789 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-7115     TCGA-EJ-7314 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7792 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332     TCGA-G9-6333 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342     TCGA-G9-6343 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6365 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377     TCGA-G9-6378 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494     TCGA-G9-6496 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075     TCGA-HC-7077 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7081 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231     TCGA-HC-7232 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7820     TCGA-HI-7168     TCGA-HI-7169 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 

Clustering(15) Variable = GATA6 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2               0   1
  GATA6 MUTATED     4   0
  GATA6 WILD-TYPE 484  10
  GATA6 MUTATED GATA6 WILD-TYPE 
              4             494 
  GATA6 MUTATED GATA6 WILD-TYPE 
              0              10 
$`GATA6 MUTATED`
TCGA-HC-7821 TCGA-HC-A8D1 TCGA-V1-A9Z9 TCGA-XK-AAJT 
       31.43        18.84        17.75        47.15 

$`GATA6 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A9TE 
        1.25         4.41         4.93         9.53        25.48        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       35.08        28.73        27.19        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJU 
       37.25        40.04        30.58        41.39        36.95        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  GATA6 MUTATED GATA6 WILD-TYPE 
          17.75            0.76 
  GATA6 MUTATED GATA6 WILD-TYPE 
          47.15          165.17 
  GATA6 MUTATED GATA6 WILD-TYPE 
         25.135          30.445 
[1] "17.8 - 47.1 (25.1)" "0.8 - 165.2 (30.4)"
[1] "hr="     "3300000"
D15V2, continuous
                 vv
clus               T2  T3  T4
  GATA6 MUTATED     2   2   0
  GATA6 WILD-TYPE 186 291  10
D15V3, multiclass
    clus
vv   GATA6 MUTATED GATA6 WILD-TYPE
  T2             2             186
  T3             2             291
  T4             0              10
[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
  GATA6 MUTATED     3   1
  GATA6 WILD-TYPE 343  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      3    1
  GATA6 WILD-TYPE  343   78
   clus
vv  GATA6 MUTATED GATA6 WILD-TYPE
  0             3             343
  1             1              78
[1] 2 2
[1] FALSE
D15V5, binary
                 cls
clus                0   1
  GATA6 MUTATED     3   1
  GATA6 WILD-TYPE 392  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      3    1
  GATA6 WILD-TYPE  392   58
     clus
vv    GATA6 MUTATED GATA6 WILD-TYPE
  NO              3             392
  YES             1              58
[1] 2 2
[1] FALSE
D15V6, binary
                 cls
clus                0   1
  GATA6 MUTATED     4   0
  GATA6 WILD-TYPE 479  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GATA6 MUTATED      4    0
  GATA6 WILD-TYPE  479   15
                                        clus
vv                                       GATA6 MUTATED GATA6 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  GATA6 MUTATED     2   1   0   0
  GATA6 WILD-TYPE 314 146   5  15
D15V7, multiclass
    clus
vv   GATA6 MUTATED GATA6 WILD-TYPE
  R0             2             314
  R1             1             146
  R2             0               5
  RX             0              15
[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
  GATA6 MUTATED       0                         0     1
  GATA6 WILD-TYPE     2                         7   146
D15V11, multiclass
[1] "Remove cluster labels:" "GATA6 MUTATED"         
clus
  GATA6 MUTATED GATA6 WILD-TYPE 
              1             155 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788      TCGA-CH-5789 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115      TCGA-EJ-7125 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7747      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"GATA6 WILD-TYPE" "GATA6 WILD-TYPE" "GATA6 WILD-TYPE" 

Clustering(16) Variable = SMG7 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2              0   1
  SMG7 MUTATED     8   0
  SMG7 WILD-TYPE 480  10
  SMG7 MUTATED SMG7 WILD-TYPE 
             8            490 
  SMG7 MUTATED SMG7 WILD-TYPE 
             0             10 
$`SMG7 MUTATED`
TCGA-EJ-7325 TCGA-2A-A8VX TCGA-CH-5737 TCGA-EJ-A8FS TCGA-HC-7742 TCGA-HI-7169 
       35.18        45.30         2.99         8.75        30.84        88.24 
TCGA-KK-A59V TCGA-XK-AAIW 
      113.10        40.04 

$`SMG7 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       49.74        84.56        36.13        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        45.14        22.06         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5738 TCGA-CH-5739 
       44.84        41.82        20.22        11.51         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 
        1.02        12.99        13.97         1.97         2.99        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 
        1.02        13.02        35.01        31.00         2.04         0.92 
TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       44.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
       13.02        26.99         9.99         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        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        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-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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU 
        4.21         6.48        10.82         9.27         9.83         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       32.68        26.01        29.79        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       23.57        17.46        23.70        24.59        23.80        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87        27.85        30.38        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        15.55        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7170 
       25.48        18.84        19.30        27.75       109.25        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
        5.85         6.97        10.62        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
       21.86         2.99         8.65         8.88        11.57        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       64.70        86.40        81.17       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        57.67 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 
       49.94        43.69        34.95        36.13        74.27       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC 
       21.96        65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       67.46        20.65        62.96        16.21        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC 
       13.15        34.85        25.08        29.23        18.84         5.69 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK 
        3.19       140.19       122.17        86.14        18.12         0.89 
TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       17.29        20.05        47.64        28.18        58.88        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        61.68        64.04        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 
       22.55        35.44         6.64        63.52        82.16        94.36 
TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT 
       20.91        38.93        79.00        62.89        12.20        15.65 
TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG 
       37.28        35.08        28.73        27.19        17.75        49.87 
TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       53.92        45.47        44.75         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        25.18        15.81        41.42        44.91        25.78 
TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
       31.99        31.96        37.25        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  SMG7 MUTATED SMG7 WILD-TYPE 
          2.99           0.76 
  SMG7 MUTATED SMG7 WILD-TYPE 
        113.10         165.17 
  SMG7 MUTATED SMG7 WILD-TYPE 
        37.610         30.365 
[1] "3.0 - 113.1 (37.6)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9400000"
D16V2, continuous
                vv
clus              T2  T3  T4
  SMG7 MUTATED     1   7   0
  SMG7 WILD-TYPE 187 286  10
D16V3, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  T2            1            187
  T3            7            286
  T4            0             10
[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
  SMG7 MUTATED     8   0
  SMG7 WILD-TYPE 338  79
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      8    0
  SMG7 WILD-TYPE  338   79
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            8            338
  1            0             79
[1] 2 2
[1] FALSE
D16V5, binary
                cls
clus               0   1
  SMG7 MUTATED     7   0
  SMG7 WILD-TYPE 388  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      7    0
  SMG7 WILD-TYPE  388   59
     clus
vv    SMG7 MUTATED SMG7 WILD-TYPE
  NO             7            388
  YES            0             59
[1] 2 2
[1] FALSE
D16V6, binary
                cls
clus               0   1
  SMG7 MUTATED     8   0
  SMG7 WILD-TYPE 475  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      8    0
  SMG7 WILD-TYPE  475   15
                                        clus
vv                                       SMG7 MUTATED SMG7 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               8            475
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMG7 MUTATED     6   2   0   0
  SMG7 WILD-TYPE 310 145   5  15
D16V7, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  R0            6            310
  R1            2            145
  R2            0              5
  RX            0             15
[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
D16V9, continuous
D16V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMG7 MUTATED       0                         0     3
  SMG7 WILD-TYPE     2                         7   144
D16V11, multiclass
                           clus
vv                          SMG7 MUTATED SMG7 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            144
[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 = CNTNAP1 MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  CNTNAP1 MUTATED     9   0
  CNTNAP1 WILD-TYPE 479  10
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                9               489 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                0                10 
$`CNTNAP1 MUTATED`
TCGA-EJ-A65M TCGA-HC-8256 TCGA-HC-8265 TCGA-HC-8266 TCGA-J9-A52D TCGA-KC-A7F6 
        7.56        28.27        15.88        15.55         6.97         8.65 
TCGA-XJ-A9DX TCGA-XK-AAIW TCGA-ZG-A9L1 
       31.99        40.04        42.81 

$`CNTNAP1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       18.41        21.90        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8257 
       30.84        17.85        24.56        19.36        22.42        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        22.55        17.95        22.32         1.58 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       27.12        13.87         5.85        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66        21.86         2.99         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR 
        2.99        31.96        37.25        30.58        41.39        36.95 
TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI 
       47.15        51.81         4.80        25.32        32.61        17.29 
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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX 
       70.22        24.33        49.91        36.10         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       13.28        10.13         4.27        11.67        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
             6.97              0.76 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
            42.81            165.17 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
            15.88             30.58 
[1] "7.0 - 42.8 (15.9)"  "0.8 - 165.2 (30.6)"
[1] "hr="     "3300000"
D17V2, continuous
                   vv
clus                 T2  T3  T4
  CNTNAP1 MUTATED     3   6   0
  CNTNAP1 WILD-TYPE 185 287  10
D17V3, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  T2               3               185
  T3               6               287
  T4               0                10
[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
  CNTNAP1 MUTATED     5   2
  CNTNAP1 WILD-TYPE 341  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      5    2
  CNTNAP1 WILD-TYPE  341   77
   clus
vv  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  0               5               341
  1               2                77
[1] 2 2
[1] FALSE
D17V5, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     6   2
  CNTNAP1 WILD-TYPE 389  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      6    2
  CNTNAP1 WILD-TYPE  389   57
     clus
vv    CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  NO                6               389
  YES               2                57
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     8   1
  CNTNAP1 WILD-TYPE 475  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      8    1
  CNTNAP1 WILD-TYPE  475   14
                                        clus
vv                                       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  8               475
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               1                14
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CNTNAP1 MUTATED     3   5   0   0
  CNTNAP1 WILD-TYPE 313 142   5  15
D17V7, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  R0               3               313
  R1               5               142
  R2               0                 5
  RX               0                15
[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
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP1 MUTATED       0                         0     0
  CNTNAP1 WILD-TYPE     2                         7   147
D17V11, multiclass

Clustering(18) Variable = CDKN1B MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  CDKN1B MUTATED     6   0
  CDKN1B WILD-TYPE 482  10
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               6              492 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               0               10 
$`CDKN1B MUTATED`
TCGA-CH-5752 TCGA-EJ-5518 TCGA-EJ-7786 TCGA-KK-A59V TCGA-V1-A9OQ TCGA-VP-A87J 
       31.00        69.63        36.03       113.10        12.20        58.32 

$`CDKN1B WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5519 
       56.98        60.13        60.23        62.10        62.10        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        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 
       25.68        38.70        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        45.30        44.81        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       28.18        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       13.55        27.12        13.87         5.85         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       62.89        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  CDKN1B MUTATED CDKN1B WILD-TYPE 
           12.20             0.76 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
          113.10           165.17 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
          47.175           30.365 
[1] "12.2 - 113.1 (47.2)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "9200000"
D18V2, continuous
                  vv
clus                T2  T3  T4
  CDKN1B MUTATED     1   4   1
  CDKN1B WILD-TYPE 187 289   9
D18V3, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  T2              1              187
  T3              4              289
  T4              1                9
[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
  CDKN1B MUTATED     4   1
  CDKN1B WILD-TYPE 342  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      4    1
  CDKN1B WILD-TYPE  342   78
   clus
vv  CDKN1B MUTATED CDKN1B WILD-TYPE
  0              4              342
  1              1               78
[1] 2 2
[1] FALSE
D18V5, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     5   1
  CDKN1B WILD-TYPE 390  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      5    1
  CDKN1B WILD-TYPE  390   58
     clus
vv    CDKN1B MUTATED CDKN1B WILD-TYPE
  NO               5              390
  YES              1               58
[1] 2 2
[1] FALSE
D18V6, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     6   0
  CDKN1B WILD-TYPE 477  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      6    0
  CDKN1B WILD-TYPE  477   15
                                        clus
vv                                       CDKN1B MUTATED CDKN1B WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 6              477
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDKN1B MUTATED     3   2   1   0
  CDKN1B WILD-TYPE 313 145   4  15
D18V7, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  R0              3              313
  R1              2              145
  R2              1                4
  RX              0               15
[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
  CDKN1B MUTATED       0                         0     3
  CDKN1B WILD-TYPE     2                         7   144
D18V11, multiclass
                           clus
vv                          CDKN1B MUTATED CDKN1B WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[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(19) Variable = EOMES MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  EOMES MUTATED     5   0
  EOMES WILD-TYPE 483  10
  EOMES MUTATED EOMES WILD-TYPE 
              5             493 
  EOMES MUTATED EOMES WILD-TYPE 
              0              10 
$`EOMES MUTATED`
TCGA-EJ-5508 TCGA-G9-6365 TCGA-G9-7523 TCGA-J9-A52C TCGA-QU-A6IO 
       64.60        44.81        28.18         5.85       122.17 

$`EOMES WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        45.40        47.90        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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6366 
       67.92        47.15        46.52        47.44        45.30        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       13.55        27.12        13.87         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IP 
       29.23        18.84         5.69         3.19       140.19        86.14 
TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG 
       18.12         0.89        17.29        20.05        47.64        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       58.88        16.70        14.73        39.29        61.68        64.04 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 
       30.38        15.58        22.55        35.44         6.64        63.52 
TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL 
       82.16        94.36        20.91        38.93        79.00        62.89 
TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 
       12.20        15.65        37.28        35.08        28.73        27.19 
TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       17.75        49.87        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        58.32        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  EOMES MUTATED EOMES WILD-TYPE 
           5.85            0.76 
  EOMES MUTATED EOMES WILD-TYPE 
         122.17          165.17 
  EOMES MUTATED EOMES WILD-TYPE 
          44.81           30.38 
[1] "5.8 - 122.2 (44.8)" "0.8 - 165.2 (30.4)"
[1] "hr="     "2.9e+07"
D19V2, continuous
                 vv
clus               T2  T3  T4
  EOMES MUTATED     1   3   1
  EOMES WILD-TYPE 187 290   9
D19V3, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  T2             1             187
  T3             3             290
  T4             1               9
[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
  EOMES MUTATED     4   0
  EOMES WILD-TYPE 342  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      4    0
  EOMES WILD-TYPE  342   79
   clus
vv  EOMES MUTATED EOMES WILD-TYPE
  0             4             342
  1             0              79
[1] 2 2
[1] FALSE
D19V5, binary
                 cls
clus                0   1
  EOMES MUTATED     5   0
  EOMES WILD-TYPE 390  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      5    0
  EOMES WILD-TYPE  390   59
     clus
vv    EOMES MUTATED EOMES WILD-TYPE
  NO              5             390
  YES             0              59
[1] 2 2
[1] FALSE
D19V6, binary
                 cls
clus                0   1
  EOMES MUTATED     5   0
  EOMES WILD-TYPE 478  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EOMES MUTATED      5    0
  EOMES WILD-TYPE  478   15
                                        clus
vv                                       EOMES MUTATED EOMES WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  EOMES MUTATED     2   3   0   0
  EOMES WILD-TYPE 314 144   5  15
D19V7, multiclass
    clus
vv   EOMES MUTATED EOMES WILD-TYPE
  R0             2             314
  R1             3             144
  R2             0               5
  RX             0              15
[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
  EOMES MUTATED       0                         0     2
  EOMES WILD-TYPE     2                         7   145
D19V11, multiclass
[1] "Remove cluster labels:" "EOMES MUTATED"         
clus
  EOMES MUTATED EOMES WILD-TYPE 
              2             154 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5509 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115      TCGA-EJ-7125 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231      TCGA-HC-7232 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168      TCGA-HI-7169 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" "EOMES WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"EOMES WILD-TYPE" "EOMES WILD-TYPE" 

Clustering(20) Variable = NBPF1 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2               0   1
  NBPF1 MUTATED     9   0
  NBPF1 WILD-TYPE 479  10
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              9             489 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
              0              10 
$`NBPF1 MUTATED`
TCGA-HC-7233 TCGA-G9-6356 TCGA-HC-7081 TCGA-HC-8256 TCGA-XK-AAIW TCGA-XK-AAJA 
       44.55        47.15        37.35        28.27        40.04        30.58 
TCGA-YL-A8SI TCGA-ZG-A9KY TCGA-ZG-A9ND 
       53.06         4.27        13.48 

$`NBPF1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7748 TCGA-HC-7821 
       21.96        14.83        28.70        39.39        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       67.92        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       38.93        36.36        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       24.56        19.36        22.42        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       27.12        13.87         5.85         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       14.53        13.28        10.13        11.67        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9NI 
       14.96        11.47         4.34 

  NBPF1 MUTATED NBPF1 WILD-TYPE 
           4.27            0.76 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          53.06          165.17 
  NBPF1 MUTATED NBPF1 WILD-TYPE 
          37.35           30.38 
[1] "4.3 - 53.1 (37.4)"  "0.8 - 165.2 (30.4)"
[1] "hr="     "9200000"
D20V2, continuous
                 vv
clus               T2  T3  T4
  NBPF1 MUTATED     2   6   1
  NBPF1 WILD-TYPE 186 287   9
D20V3, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  T2             2             186
  T3             6             287
  T4             1               9
[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
  NBPF1 MUTATED     6   1
  NBPF1 WILD-TYPE 340  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      6    1
  NBPF1 WILD-TYPE  340   78
   clus
vv  NBPF1 MUTATED NBPF1 WILD-TYPE
  0             6             340
  1             1              78
[1] 2 2
[1] FALSE
D20V5, binary
                 cls
clus                0   1
  NBPF1 MUTATED     8   1
  NBPF1 WILD-TYPE 387  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      8    1
  NBPF1 WILD-TYPE  387   58
     clus
vv    NBPF1 MUTATED NBPF1 WILD-TYPE
  NO              8             387
  YES             1              58
[1] 2 2
[1] FALSE
D20V6, binary
                 cls
clus                0   1
  NBPF1 MUTATED     9   0
  NBPF1 WILD-TYPE 474  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NBPF1 MUTATED      9    0
  NBPF1 WILD-TYPE  474   15
                                        clus
vv                                       NBPF1 MUTATED NBPF1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                9             474
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  NBPF1 MUTATED     4   4   1   0
  NBPF1 WILD-TYPE 312 143   4  15
D20V7, multiclass
    clus
vv   NBPF1 MUTATED NBPF1 WILD-TYPE
  R0             4             312
  R1             4             143
  R2             1               4
  RX             0              15
[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
D20V9, continuous
D20V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NBPF1 MUTATED       0                         0     3
  NBPF1 WILD-TYPE     2                         7   144
D20V11, multiclass
                           clus
vv                          NBPF1 MUTATED NBPF1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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 = LMOD2 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  LMOD2 MUTATED     6   0
  LMOD2 WILD-TYPE 482  10
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              6             492 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              0              10 
$`LMOD2 MUTATED`
TCGA-EJ-A46B TCGA-EJ-A8FN TCGA-G9-A9S7 TCGA-HC-7212 TCGA-J4-A67Q TCGA-J9-A8CM 
       21.60        10.82        23.93        28.60        32.05        15.22 

$`LMOD2 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46G 
       49.74        84.56        36.13        35.18        36.76        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FP 
        6.48        15.65         4.21         6.48         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        29.79         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
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        40.14        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        30.81        27.58        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         2.99         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  LMOD2 MUTATED LMOD2 WILD-TYPE 
          10.82            0.76 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
          32.05          165.17 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
         22.765          30.645 
[1] "10.8 - 32.0 (22.8)" "0.8 - 165.2 (30.6)"
[1] "hr="     "3300000"
D21V2, continuous
                 vv
clus               T2  T3  T4
  LMOD2 MUTATED     3   3   0
  LMOD2 WILD-TYPE 185 290  10
D21V3, multiclass
    clus
vv   LMOD2 MUTATED LMOD2 WILD-TYPE
  T2             3             185
  T3             3             290
  T4             0              10
[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
  LMOD2 MUTATED     4   1
  LMOD2 WILD-TYPE 342  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      4    1
  LMOD2 WILD-TYPE  342   78
   clus
vv  LMOD2 MUTATED LMOD2 WILD-TYPE
  0             4             342
  1             1              78
[1] 2 2
[1] FALSE
D21V5, binary
                 cls
clus                0   1
  LMOD2 MUTATED     4   1
  LMOD2 WILD-TYPE 391  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      4    1
  LMOD2 WILD-TYPE  391   58
     clus
vv    LMOD2 MUTATED LMOD2 WILD-TYPE
  NO              4             391
  YES             1              58
[1] 2 2
[1] FALSE
D21V6, binary
                 cls
clus                0   1
  LMOD2 MUTATED     6   0
  LMOD2 WILD-TYPE 477  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      6    0
  LMOD2 WILD-TYPE  477   15
                                        clus
vv                                       LMOD2 MUTATED LMOD2 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             477
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMOD2 MUTATED     3   1   0   0
  LMOD2 WILD-TYPE 313 146   5  15
D21V7, multiclass
    clus
vv   LMOD2 MUTATED LMOD2 WILD-TYPE
  R0             3             313
  R1             1             146
  R2             0               5
  RX             0              15
[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
  LMOD2 MUTATED       0                         0     1
  LMOD2 WILD-TYPE     2                         7   146
D21V11, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              1             155 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7789      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7747      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 

Clustering(22) Variable = EHHADH MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  EHHADH MUTATED     5   0
  EHHADH WILD-TYPE 483  10
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              493 
  EHHADH MUTATED EHHADH WILD-TYPE 
               0               10 
$`EHHADH MUTATED`
TCGA-CH-5752 TCGA-HC-7745 TCGA-V1-A8MU TCGA-VP-A87B TCGA-YL-A8SC 
       31.00        23.70        61.68        89.49        41.46 

$`EHHADH WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       39.29        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       119.38 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D 
       75.91       109.58       102.90        23.93        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        56.52        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  EHHADH MUTATED EHHADH WILD-TYPE 
           23.70             0.76 
  EHHADH MUTATED EHHADH WILD-TYPE 
           89.49           165.17 
  EHHADH MUTATED EHHADH WILD-TYPE 
           41.46            30.38 
[1] "23.7 - 89.5 (41.5)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9200000"
D22V2, continuous
                  vv
clus                T2  T3  T4
  EHHADH MUTATED     1   4   0
  EHHADH WILD-TYPE 187 289  10
D22V3, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  T2              1              187
  T3              4              289
  T4              0               10
[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
  EHHADH MUTATED     4   1
  EHHADH WILD-TYPE 342  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      4    1
  EHHADH WILD-TYPE  342   78
   clus
vv  EHHADH MUTATED EHHADH WILD-TYPE
  0              4              342
  1              1               78
[1] 2 2
[1] FALSE
D22V5, binary
                  cls
clus                 0   1
  EHHADH MUTATED     3   2
  EHHADH WILD-TYPE 392  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      3    2
  EHHADH WILD-TYPE  392   57
     clus
vv    EHHADH MUTATED EHHADH WILD-TYPE
  NO               3              392
  YES              2               57
[1] 2 2
[1] FALSE
D22V6, binary
                  cls
clus                 0   1
  EHHADH MUTATED     5   0
  EHHADH WILD-TYPE 478  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      5    0
  EHHADH WILD-TYPE  478   15
                                        clus
vv                                       EHHADH MUTATED EHHADH WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EHHADH MUTATED     3   2   0   0
  EHHADH WILD-TYPE 313 145   5  15
D22V7, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  R0              3              313
  R1              2              145
  R2              0                5
  RX              0               15
[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
  EHHADH MUTATED       0                         0     2
  EHHADH WILD-TYPE     2                         7   145
D22V11, multiclass
[1] "Remove cluster labels:" "EHHADH MUTATED"        
clus
  EHHADH MUTATED EHHADH WILD-TYPE 
               2              154 
      TCGA-CH-5753       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5772 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-EJ-5542       TCGA-EJ-7123 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7791       TCGA-G9-6364       TCGA-HC-7233       TCGA-HC-7748 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7821       TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5740       TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5745       TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5751       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5788       TCGA-CH-5789 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494       TCGA-EJ-5495 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498       TCGA-EJ-5499 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504       TCGA-EJ-5505 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508       TCGA-EJ-5509 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512       TCGA-EJ-5514 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517       TCGA-EJ-5518 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522       TCGA-EJ-5524 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527       TCGA-EJ-5530 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-7115       TCGA-EJ-7125 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7736       TCGA-HC-7737       TCGA-HC-7738 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7742       TCGA-HC-7744       TCGA-HC-7747 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HI-7168       TCGA-HI-7169 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 

Clustering(23) Variable = MED12 MUTATION ANALYSIS
D23V1, survival
                 sevent
clus2               0   1
  MED12 MUTATED     8   0
  MED12 WILD-TYPE 480  10
  MED12 MUTATED MED12 WILD-TYPE 
              8             490 
  MED12 MUTATED MED12 WILD-TYPE 
              0              10 
$`MED12 MUTATED`
TCGA-CH-5748 TCGA-EJ-5510 TCGA-G9-6362 TCGA-G9-7519 TCGA-HC-A6AL TCGA-KC-A7F3 
        1.02        62.04        47.44        27.91         2.20        21.86 
TCGA-VP-A87J TCGA-YL-A9WY 
       58.32        36.10 

$`MED12 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97         2.99        24.03        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 TCGA-EJ-5512 
       45.40        47.90        64.60        48.13        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        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.15        46.52        45.30        44.81        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        52.93        38.96        30.97        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       32.68        26.01        29.79        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         1.78         2.01         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       43.66         2.99         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP 
       31.99        31.96        37.25        40.04        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-ZG-A8QW TCGA-ZG-A8QX 
       60.99        70.22        24.33        49.91         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 
       13.28        10.13         4.27        11.67        42.81        37.94 
TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM 
       36.43        29.85        22.59        20.28        19.17        12.43 
TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 
        3.78        16.96        19.04        12.16        22.75        17.98 
TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       14.96        11.47        13.48         4.34 

  MED12 MUTATED MED12 WILD-TYPE 
           1.02            0.76 
  MED12 MUTATED MED12 WILD-TYPE 
          62.04          165.17 
  MED12 MUTATED MED12 WILD-TYPE 
         32.005          30.445 
[1] "1.0 - 62.0 (32.0)"  "0.8 - 165.2 (30.4)"
[1] "hr="     "9100000"
D23V2, continuous
                 vv
clus               T2  T3  T4
  MED12 MUTATED     4   4   0
  MED12 WILD-TYPE 184 289  10
D23V3, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  T2             4             184
  T3             4             289
  T4             0              10
[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"
D23V4, binary
                 cls
clus                0   1
  MED12 MUTATED     5   2
  MED12 WILD-TYPE 341  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      5    2
  MED12 WILD-TYPE  341   77
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             5             341
  1             2              77
[1] 2 2
[1] FALSE
D23V5, binary
                 cls
clus                0   1
  MED12 MUTATED     6   0
  MED12 WILD-TYPE 389  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      6    0
  MED12 WILD-TYPE  389   59
     clus
vv    MED12 MUTATED MED12 WILD-TYPE
  NO              6             389
  YES             0              59
[1] 2 2
[1] FALSE
D23V6, binary
                 cls
clus                0   1
  MED12 MUTATED     8   0
  MED12 WILD-TYPE 475  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      8    0
  MED12 WILD-TYPE  475   15
                                        clus
vv                                       MED12 MUTATED MED12 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                8             475
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED12 MUTATED     4   3   1   0
  MED12 WILD-TYPE 312 144   4  15
D23V7, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0             4             312
  R1             3             144
  R2             1               4
  RX             0              15
[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"
D23V8, continuous
D23V9, continuous
D23V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED       0                         0     3
  MED12 WILD-TYPE     2                         7   144
D23V11, multiclass
                           clus
vv                          MED12 MUTATED MED12 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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(24) Variable = ZNF709 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  ZNF709 MUTATED     5   0
  ZNF709 WILD-TYPE 483  10
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              493 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               0               10 
$`ZNF709 MUTATED`
TCGA-EJ-7328 TCGA-EJ-8469 TCGA-HC-7744 TCGA-KK-A59V TCGA-XJ-A9DI 
       27.68        76.41        17.46       113.10        48.03 

$`ZNF709 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       27.09        30.35         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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       45.90         3.75        42.94        32.32        77.16        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 
       35.84        31.69        23.57        30.84        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       13.55        27.12        13.87         5.85         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW 
        9.04         2.99        31.99        31.96        37.25        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
           17.46             0.76 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
          113.10           165.17 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
           48.03            30.38 
[1] "17.5 - 113.1 (48.0)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "9200000"
D24V2, continuous
                  vv
clus                T2  T3  T4
  ZNF709 MUTATED     0   5   0
  ZNF709 WILD-TYPE 188 288  10
D24V3, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  T2              0              188
  T3              5              288
  T4              0               10
[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"
D24V4, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     5   0
  ZNF709 WILD-TYPE 341  79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      5    0
  ZNF709 WILD-TYPE  341   79
   clus
vv  ZNF709 MUTATED ZNF709 WILD-TYPE
  0              5              341
  1              0               79
[1] 2 2
[1] FALSE
D24V5, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     3   2
  ZNF709 WILD-TYPE 392  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      3    2
  ZNF709 WILD-TYPE  392   57
     clus
vv    ZNF709 MUTATED ZNF709 WILD-TYPE
  NO               3              392
  YES              2               57
[1] 2 2
[1] FALSE
D24V6, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     5   0
  ZNF709 WILD-TYPE 478  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      5    0
  ZNF709 WILD-TYPE  478   15
                                        clus
vv                                       ZNF709 MUTATED ZNF709 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF709 MUTATED     3   1   0   1
  ZNF709 WILD-TYPE 313 146   5  14
D24V7, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  R0              3              313
  R1              1              146
  R2              0                5
  RX              1               14
[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"
D24V8, continuous
D24V9, continuous
D24V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF709 MUTATED       0                         0     2
  ZNF709 WILD-TYPE     2                         7   145
D24V11, multiclass
[1] "Remove cluster labels:" "ZNF709 MUTATED"        
clus
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               2              154 
      TCGA-CH-5753       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5772 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-EJ-5542       TCGA-EJ-7123 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7791       TCGA-G9-6364       TCGA-HC-7233       TCGA-HC-7748 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7821       TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5740       TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5745       TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5754       TCGA-CH-5761 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5788 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-7115 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7125       TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7321       TCGA-EJ-7327       TCGA-EJ-7330       TCGA-EJ-7331 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7736       TCGA-HC-7737       TCGA-HC-7738 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7742       TCGA-HC-7745       TCGA-HC-7747 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HI-7168       TCGA-HI-7169 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 

Clustering(25) Variable = TCEB3 MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2               0   1
  TCEB3 MUTATED     4   0
  TCEB3 WILD-TYPE 484  10
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             494 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              0              10 
$`TCEB3 MUTATED`
TCGA-CH-5766 TCGA-EJ-5530 TCGA-J9-A52B TCGA-J9-A52C 
        1.02        60.23        13.87         5.85 

$`TCEB3 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5767 
       31.00         2.04         0.92        44.02        23.01        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       58.45        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       18.18        13.55        27.12         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  TCEB3 MUTATED TCEB3 WILD-TYPE 
           1.02            0.76 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
          60.23          165.17 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
          9.860          30.545 
[1] "1.0 - 60.2 (9.9)"   "0.8 - 165.2 (30.5)"
[1] "hr="     "1200000"
D25V2, continuous
                 vv
clus               T2  T3  T4
  TCEB3 MUTATED     1   3   0
  TCEB3 WILD-TYPE 187 290  10
D25V3, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  T2             1             187
  T3             3             290
  T4             0              10
[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"
D25V4, binary
                 cls
clus                0   1
  TCEB3 MUTATED     2   1
  TCEB3 WILD-TYPE 344  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      2    1
  TCEB3 WILD-TYPE  344   78
   clus
vv  TCEB3 MUTATED TCEB3 WILD-TYPE
  0             2             344
  1             1              78
[1] 2 2
[1] FALSE
D25V5, binary
                 cls
clus                0   1
  TCEB3 MUTATED     3   0
  TCEB3 WILD-TYPE 392  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      3    0
  TCEB3 WILD-TYPE  392   59
     clus
vv    TCEB3 MUTATED TCEB3 WILD-TYPE
  NO              3             392
  YES             0              59
[1] 2 2
[1] FALSE
D25V6, binary
                 cls
clus                0   1
  TCEB3 MUTATED     4   0
  TCEB3 WILD-TYPE 479  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      4    0
  TCEB3 WILD-TYPE  479   15
                                        clus
vv                                       TCEB3 MUTATED TCEB3 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TCEB3 MUTATED     3   1   0   0
  TCEB3 WILD-TYPE 313 146   5  15
D25V7, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  R0             3             313
  R1             1             146
  R2             0               5
  RX             0              15
[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"
D25V8, continuous
D25V9, continuous
D25V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCEB3 MUTATED       0                         0     2
  TCEB3 WILD-TYPE     2                         7   145
D25V11, multiclass
[1] "Remove cluster labels:" "TCEB3 MUTATED"         
clus
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              2             154 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5767      TCGA-CH-5768 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788      TCGA-CH-5789 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5531 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5532      TCGA-EJ-7115      TCGA-EJ-7125      TCGA-EJ-7314 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7792 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6365 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7212 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231      TCGA-HC-7232 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168      TCGA-HI-7169 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 

Clustering(26) Variable = MED15 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  MED15 MUTATED     7   0
  MED15 WILD-TYPE 481  10
  MED15 MUTATED MED15 WILD-TYPE 
              7             491 
  MED15 MUTATED MED15 WILD-TYPE 
              0              10 
$`MED15 MUTATED`
TCGA-CH-5764 TCGA-EJ-7782 TCGA-G9-7523 TCGA-HC-7211 TCGA-J4-A83M TCGA-KK-A59V 
        1.02        38.37        28.18        40.14        17.85       113.10 
TCGA-XK-AAIW 
       40.04 

$`MED15 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        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-7783 
       30.35        27.68         6.28        24.39        35.28        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       35.44        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 
       36.36        37.35        14.47        28.54        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       22.88        10.78        23.67        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         2.99         8.65         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP 
        2.99        31.99        31.96        37.25        30.58        41.39 
TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL 
       36.95        47.15        51.81         4.80        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW 
       60.99        70.22        24.33        49.91        36.10         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 
       14.53        13.28        10.13         4.27        11.67        42.81 
TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB 
       37.94        36.43        29.85        22.59        20.28        19.17 
TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ 
       12.43         3.78        16.96        19.04        12.16        22.75 
TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       17.98        14.96        11.47        13.48         4.34 

  MED15 MUTATED MED15 WILD-TYPE 
           1.02            0.76 
  MED15 MUTATED MED15 WILD-TYPE 
         113.10          165.17 
  MED15 MUTATED MED15 WILD-TYPE 
          38.37           30.38 
[1] "1.0 - 113.1 (38.4)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9200000"
D26V2, continuous
                 vv
clus               T2  T3  T4
  MED15 MUTATED     3   4   0
  MED15 WILD-TYPE 185 289  10
D26V3, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  T2             3             185
  T3             4             289
  T4             0              10
[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"
D26V4, binary
                 cls
clus                0   1
  MED15 MUTATED     7   0
  MED15 WILD-TYPE 339  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      7    0
  MED15 WILD-TYPE  339   79
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0             7             339
  1             0              79
[1] 2 2
[1] FALSE
D26V5, binary
                 cls
clus                0   1
  MED15 MUTATED     5   1
  MED15 WILD-TYPE 390  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      5    1
  MED15 WILD-TYPE  390   58
     clus
vv    MED15 MUTATED MED15 WILD-TYPE
  NO              5             390
  YES             1              58
[1] 2 2
[1] FALSE
D26V6, binary
                 cls
clus                0   1
  MED15 MUTATED     7   0
  MED15 WILD-TYPE 476  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      7    0
  MED15 WILD-TYPE  476   15
                                        clus
vv                                       MED15 MUTATED MED15 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             476
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED15 MUTATED     4   3   0   0
  MED15 WILD-TYPE 312 144   5  15
D26V7, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  R0             4             312
  R1             3             144
  R2             0               5
  RX             0              15
[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"
D26V8, continuous
D26V9, continuous
D26V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED15 MUTATED       0                         1     2
  MED15 WILD-TYPE     2                         6   145
D26V11, multiclass
                           clus
vv                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 2             145
[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(27) Variable = ERF MUTATION ANALYSIS
D27V1, survival
               sevent
clus2             0   1
  ERF MUTATED     5   0
  ERF WILD-TYPE 483  10
  ERF MUTATED ERF WILD-TYPE 
            5           493 
  ERF MUTATED ERF WILD-TYPE 
            0            10 
$`ERF MUTATED`
TCGA-KC-A7F5 TCGA-KK-A59V TCGA-V1-A9ZR TCGA-XK-AAIW TCGA-YL-A8SB 
        2.99       113.10        44.75        40.04        56.52 

$`ERF WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
        5.85         6.97        10.62        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
       21.86         8.65         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       45.47         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ 
       16.83        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  ERF MUTATED ERF WILD-TYPE 
         2.99          0.76 
  ERF MUTATED ERF WILD-TYPE 
       113.10        165.17 
  ERF MUTATED ERF WILD-TYPE 
        44.75         30.38 
[1] "3.0 - 113.1 (44.8)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9200000"
D27V2, continuous
               vv
clus             T2  T3  T4
  ERF MUTATED     1   3   1
  ERF WILD-TYPE 187 290   9
D27V3, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  T2           1           187
  T3           3           290
  T4           1             9
[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"
D27V4, binary
               cls
clus              0   1
  ERF MUTATED     5   0
  ERF WILD-TYPE 341  79
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      5    0
  ERF WILD-TYPE  341   79
   clus
vv  ERF MUTATED ERF WILD-TYPE
  0           5           341
  1           0            79
[1] 2 2
[1] FALSE
D27V5, binary
               cls
clus              0   1
  ERF MUTATED     4   1
  ERF WILD-TYPE 391  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      4    1
  ERF WILD-TYPE  391   58
     clus
vv    ERF MUTATED ERF WILD-TYPE
  NO            4           391
  YES           1            58
[1] 2 2
[1] FALSE
D27V6, binary
               cls
clus              0   1
  ERF MUTATED     5   0
  ERF WILD-TYPE 478  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  ERF MUTATED      5    0
  ERF WILD-TYPE  478   15
                                        clus
vv                                       ERF MUTATED ERF WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE              5           478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE           0            15
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ERF MUTATED     2   3   0   0
  ERF WILD-TYPE 314 144   5  15
D27V7, multiclass
    clus
vv   ERF MUTATED ERF WILD-TYPE
  R0           2           314
  R1           3           144
  R2           0             5
  RX           0            15
[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"
D27V8, continuous
D27V9, continuous
D27V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERF MUTATED       0                         0     0
  ERF WILD-TYPE     2                         7   147
D27V11, multiclass

Clustering(28) Variable = ERN1 MUTATION ANALYSIS
D28V1, survival
                sevent
clus2              0   1
  ERN1 MUTATED     4   0
  ERN1 WILD-TYPE 484  10
  ERN1 MUTATED ERN1 WILD-TYPE 
             4            494 
  ERN1 MUTATED ERN1 WILD-TYPE 
             0             10 
$`ERN1 MUTATED`
TCGA-J4-A83J TCGA-KK-A7AQ TCGA-V1-A8MU TCGA-XK-AAIW 
       22.88        52.93        61.68        40.04 

$`ERN1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L 
       25.28        27.91        16.83        22.52        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        6.97        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        2.99         8.65         8.88        11.57       113.10        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       64.70        86.40        81.17       141.21        48.76        72.26 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        68.15       113.33        90.74 
TCGA-KK-A6E8 TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       58.19        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       39.29        64.04        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  ERN1 MUTATED ERN1 WILD-TYPE 
         22.88           0.76 
  ERN1 MUTATED ERN1 WILD-TYPE 
         61.68         165.17 
  ERN1 MUTATED ERN1 WILD-TYPE 
        46.485         30.380 
[1] "22.9 - 61.7 (46.5)" "0.8 - 165.2 (30.4)"
[1] "hr="     "3300000"
D28V2, continuous
                vv
clus              T2  T3  T4
  ERN1 MUTATED     2   2   0
  ERN1 WILD-TYPE 186 291  10
D28V3, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  T2            2            186
  T3            2            291
  T4            0             10
[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"
D28V4, binary
                cls
clus               0   1
  ERN1 MUTATED     3   1
  ERN1 WILD-TYPE 343  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      3    1
  ERN1 WILD-TYPE  343   78
   clus
vv  ERN1 MUTATED ERN1 WILD-TYPE
  0            3            343
  1            1             78
[1] 2 2
[1] FALSE
D28V5, binary
                cls
clus               0   1
  ERN1 MUTATED     4   0
  ERN1 WILD-TYPE 391  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      4    0
  ERN1 WILD-TYPE  391   59
     clus
vv    ERN1 MUTATED ERN1 WILD-TYPE
  NO             4            391
  YES            0             59
[1] 2 2
[1] FALSE
D28V6, binary
                cls
clus               0   1
  ERN1 MUTATED     4   0
  ERN1 WILD-TYPE 479  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      4    0
  ERN1 WILD-TYPE  479   15
                                        clus
vv                                       ERN1 MUTATED ERN1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ERN1 MUTATED     1   3   0   0
  ERN1 WILD-TYPE 315 144   5  15
D28V7, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  R0            1            315
  R1            3            144
  R2            0              5
  RX            0             15
[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"
D28V8, continuous
D28V9, continuous
D28V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERN1 MUTATED       0                         0     0
  ERN1 WILD-TYPE     2                         7   147
D28V11, multiclass

Clustering(29) Variable = MLLT10 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  MLLT10 MUTATED     5   0
  MLLT10 WILD-TYPE 483  10
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               5              493 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               0               10 
$`MLLT10 MUTATED`
TCGA-CH-5761 TCGA-EJ-5498 TCGA-EJ-5505 TCGA-EJ-5516 TCGA-XK-AAIW 
        0.92        56.55        30.31        62.10        40.04 

$`MLLT10 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       31.00         2.04        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5499 
       29.00        48.56        57.86        19.56        13.32        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 
       44.88        38.50        45.73        46.92        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-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        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        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        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-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       32.68        26.01        29.79        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X 
       17.42         2.33         1.45         1.25         4.41         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 
        9.53        25.48        18.84        19.30        27.75       109.25 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       27.12        13.87         5.85         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  MLLT10 MUTATED MLLT10 WILD-TYPE 
            0.92             0.76 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           62.10           165.17 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           40.04            30.38 
[1] "0.9 - 62.1 (40.0)"  "0.8 - 165.2 (30.4)"
[1] "hr="     "9100000"
D29V2, continuous
                  vv
clus                T2  T3  T4
  MLLT10 MUTATED     2   3   0
  MLLT10 WILD-TYPE 186 290  10
D29V3, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  T2              2              186
  T3              3              290
  T4              0               10
[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"
D29V4, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     5   0
  MLLT10 WILD-TYPE 341  79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      5    0
  MLLT10 WILD-TYPE  341   79
   clus
vv  MLLT10 MUTATED MLLT10 WILD-TYPE
  0              5              341
  1              0               79
[1] 2 2
[1] FALSE
D29V5, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     4   0
  MLLT10 WILD-TYPE 391  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      4    0
  MLLT10 WILD-TYPE  391   59
     clus
vv    MLLT10 MUTATED MLLT10 WILD-TYPE
  NO               4              391
  YES              0               59
[1] 2 2
[1] FALSE
D29V6, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     5   0
  MLLT10 WILD-TYPE 478  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      5    0
  MLLT10 WILD-TYPE  478   15
                                        clus
vv                                       MLLT10 MUTATED MLLT10 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MLLT10 MUTATED     4   1   0   0
  MLLT10 WILD-TYPE 312 146   5  15
D29V7, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  R0              4              312
  R1              1              146
  R2              0                5
  RX              0               15
[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"
D29V8, continuous
D29V9, continuous
D29V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLLT10 MUTATED       0                         0     4
  MLLT10 WILD-TYPE     2                         7   143
D29V11, multiclass
                           clus
vv                          MLLT10 MUTATED MLLT10 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  4              143
[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(30) Variable = ZFHX3 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    16   0
  ZFHX3 WILD-TYPE 472  10
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             16             482 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              0              10 
$`ZFHX3 MUTATED`
TCGA-EJ-A65J TCGA-2A-A8VX TCGA-EJ-5507 TCGA-EJ-7782 TCGA-EJ-A7NM TCGA-G9-6499 
       14.83        45.30        47.90        38.37         4.21        50.73 
TCGA-HC-7738 TCGA-HC-7820 TCGA-J9-A52C TCGA-KC-A7FD TCGA-V1-A9ZG TCGA-VN-A88R 
       31.69        24.56         5.85         8.88        49.87        25.78 
TCGA-VP-A87E TCGA-XK-AAIW TCGA-XK-AAJR TCGA-YL-A9WH 
       66.97        40.04        36.95        14.04 

$`ZFHX3 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       21.96        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        55.92        45.14        22.06         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
       22.06         1.02        12.99        13.97         1.97         2.99 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         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-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        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        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-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        24.39        35.28        25.87        25.68        38.70 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NN 
        8.22        14.20        15.58         6.48        15.65         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 
       10.82         9.27         9.83         8.75         4.54         4.31 
TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.77        28.41        15.42        28.83        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       25.94        20.25        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        80.55        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       67.33        50.70        67.92        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7509 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       38.17        36.26        35.84        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       30.84        17.85        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52D TCGA-J9-A52E 
       18.18        13.55        27.12        13.87         6.97        10.62 
TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       10.55        13.32        15.22        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I 
       27.19        17.75        53.92        45.47        44.75         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        16.31       119.38        75.91       109.58       102.90 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-A87J 
       23.93        89.49        55.56        60.92        21.80        58.32 
TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       42.94        44.88        14.76        45.47        32.19        12.36 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        48.03        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJT 
       31.99        31.96        37.25        30.58        41.39        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        45.86        46.29        32.45       114.38        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       68.48         8.98        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
           4.21            0.76 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          66.97          165.17 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          34.32           30.38 
[1] "4.2 - 67.0 (34.3)"  "0.8 - 165.2 (30.4)"
[1] "hr="     "9400000"
D30V2, continuous
                 vv
clus               T2  T3  T4
  ZFHX3 MUTATED     6  10   0
  ZFHX3 WILD-TYPE 182 283  10
D30V3, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T2             6             182
  T3            10             283
  T4             0              10
[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"
D30V4, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    10   3
  ZFHX3 WILD-TYPE 336  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     10    3
  ZFHX3 WILD-TYPE  336   76
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0            10             336
  1             3              76
[1] 2 2
[1] FALSE
D30V5, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    15   1
  ZFHX3 WILD-TYPE 380  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     15    1
  ZFHX3 WILD-TYPE  380   58
     clus
vv    ZFHX3 MUTATED ZFHX3 WILD-TYPE
  NO             15             380
  YES             1              58
[1] 2 2
[1] FALSE
D30V6, binary
                 cls
clus                0   1
  ZFHX3 MUTATED    15   1
  ZFHX3 WILD-TYPE 468  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED     15    1
  ZFHX3 WILD-TYPE  468   14
                                        clus
vv                                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               15             468
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             1              14
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    14   2   0   0
  ZFHX3 WILD-TYPE 302 145   5  15
D30V7, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            14             302
  R1             2             145
  R2             0               5
  RX             0              15
[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"
D30V8, continuous
D30V9, continuous
D30V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFHX3 MUTATED       0                         1     4
  ZFHX3 WILD-TYPE     2                         6   143
D30V11, multiclass
                           clus
vv                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 4             143
[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(31) Variable = ZMYM3 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  ZMYM3 MUTATED    12   0
  ZMYM3 WILD-TYPE 476  10
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
             12             486 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              0              10 
$`ZMYM3 MUTATED`
TCGA-CH-5772 TCGA-HC-A76W TCGA-KK-A7AP TCGA-CH-5741 TCGA-G9-6362 TCGA-KC-A4BV 
       15.98         7.00         6.44        12.99        47.44        43.66 
TCGA-KK-A59V TCGA-KK-A6E2 TCGA-KK-A7B2 TCGA-VP-AA1N TCGA-XK-AAIW TCGA-ZG-A9L0 
      113.10       165.17        36.13        44.88        40.04        11.67 

$`ZMYM3 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
        1.02        12.00         1.02        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7B3 TCGA-KK-A7B4 
        3.48        32.61        40.67        19.66        29.56        32.45 
TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO 
        2.73        41.00        41.49        32.19        20.42        55.92 
TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF 
       45.14        22.06        45.30         3.68        28.37        44.84 
TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 
       41.82        20.22        11.51         2.99         6.97        22.06 
TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 
        1.02        13.97         1.97         2.99        24.03         1.02 
TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       13.02        35.01        31.00         2.04         0.92        44.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       26.99         9.99         2.99        29.00        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-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        62.76        58.45        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 
       60.10        88.34        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-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       20.58        17.23        25.74        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90         7.56        11.61 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        4.31         4.77        28.41        15.42        28.83        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        25.94        20.25        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        80.55        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        67.33        50.70        67.92        47.15        46.52 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       45.30        44.81        64.01        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 
       27.29        58.22        56.75        64.18        50.73        52.93 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.44        28.18        32.68 
TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       26.01        29.79        23.93         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
       19.76        69.53        65.26        38.93        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        40.14        28.60        40.08        32.91 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       30.87        38.17        36.26        35.84        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
       30.84        17.46        23.70        24.59        23.80        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 
       25.71        30.51        30.84        17.85        24.56        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87        27.85        30.38        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        15.55        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
       21.86         2.99         8.65         8.88        11.57        83.34 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       64.70        86.40        81.17       141.21        48.76        72.26 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       43.69        34.95        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
           6.44            0.76 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
         165.17          141.21 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
         38.085          30.380 
[1] "6.4 - 165.2 (38.1)" "0.8 - 141.2 (30.4)"
[1] "hr="     "2.9e+07"
D31V2, continuous
                 vv
clus               T2  T3  T4
  ZMYM3 MUTATED     1  11   0
  ZMYM3 WILD-TYPE 187 282  10
D31V3, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T2             1             187
  T3            11             282
  T4             0              10
[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"
D31V4, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     8   4
  ZMYM3 WILD-TYPE 338  75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      8    4
  ZMYM3 WILD-TYPE  338   75
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0             8             338
  1             4              75
[1] 2 2
[1] FALSE
D31V5, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     7   3
  ZMYM3 WILD-TYPE 388  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      7    3
  ZMYM3 WILD-TYPE  388   56
     clus
vv    ZMYM3 MUTATED ZMYM3 WILD-TYPE
  NO              7             388
  YES             3              56
[1] 2 2
[1] FALSE
D31V6, binary
                 cls
clus                0   1
  ZMYM3 MUTATED    12   0
  ZMYM3 WILD-TYPE 471  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED     12    0
  ZMYM3 WILD-TYPE  471   15
                                        clus
vv                                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               12             471
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM3 MUTATED     4   8   0   0
  ZMYM3 WILD-TYPE 312 139   5  15
D31V7, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  R0             4             312
  R1             8             139
  R2             0               5
  RX             0              15
[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"
D31V8, continuous
D31V9, continuous
D31V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM3 MUTATED       0                         0     3
  ZMYM3 WILD-TYPE     2                         7   144
D31V11, multiclass
                           clus
vv                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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(32) Variable = FMN1 MUTATION ANALYSIS
D32V1, survival
                sevent
clus2              0   1
  FMN1 MUTATED     4   0
  FMN1 WILD-TYPE 484  10
  FMN1 MUTATED FMN1 WILD-TYPE 
             4            494 
  FMN1 MUTATED FMN1 WILD-TYPE 
             0             10 
$`FMN1 MUTATED`
TCGA-EJ-7797 TCGA-FC-A5OB TCGA-KK-A7AY TCGA-V1-A9O5 
       32.32        22.36        57.67        63.52 

$`FMN1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 
       36.33        45.90         3.75        42.94        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       15.42        28.83        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AZ TCGA-KK-A7B0 
       52.93        58.36        27.02        34.65        49.94        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  FMN1 MUTATED FMN1 WILD-TYPE 
         22.36           0.76 
  FMN1 MUTATED FMN1 WILD-TYPE 
         63.52         165.17 
  FMN1 MUTATED FMN1 WILD-TYPE 
        44.995         30.380 
[1] "22.4 - 63.5 (45.0)" "0.8 - 165.2 (30.4)"
[1] "hr="     "3300000"
D32V2, continuous
                vv
clus              T2  T3  T4
  FMN1 MUTATED     2   1   1
  FMN1 WILD-TYPE 186 292   9
D32V3, multiclass
    clus
vv   FMN1 MUTATED FMN1 WILD-TYPE
  T2            2            186
  T3            1            292
  T4            1              9
[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"
D32V4, binary
                cls
clus               0   1
  FMN1 MUTATED     3   1
  FMN1 WILD-TYPE 343  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN1 MUTATED      3    1
  FMN1 WILD-TYPE  343   78
   clus
vv  FMN1 MUTATED FMN1 WILD-TYPE
  0            3            343
  1            1             78
[1] 2 2
[1] FALSE
D32V5, binary
                cls
clus               0   1
  FMN1 MUTATED     2   2
  FMN1 WILD-TYPE 393  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN1 MUTATED      2    2
  FMN1 WILD-TYPE  393   57
     clus
vv    FMN1 MUTATED FMN1 WILD-TYPE
  NO             2            393
  YES            2             57
[1] 2 2
[1] FALSE
D32V6, binary
                cls
clus               0   1
  FMN1 MUTATED     4   0
  FMN1 WILD-TYPE 479  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  FMN1 MUTATED      4    0
  FMN1 WILD-TYPE  479   15
                                        clus
vv                                       FMN1 MUTATED FMN1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  FMN1 MUTATED     2   2   0   0
  FMN1 WILD-TYPE 314 145   5  15
D32V7, multiclass
    clus
vv   FMN1 MUTATED FMN1 WILD-TYPE
  R0            2            314
  R1            2            145
  R2            0              5
  RX            0             15
[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"
D32V8, continuous
D32V9, continuous
D32V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FMN1 MUTATED       0                         0     1
  FMN1 WILD-TYPE     2                         7   146
D32V11, multiclass
[1] "Remove cluster labels:" "FMN1 MUTATED"          
clus
  FMN1 MUTATED FMN1 WILD-TYPE 
             1            155 
    TCGA-CH-5753     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5772 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-EJ-5542     TCGA-EJ-7123 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-G9-6364     TCGA-HC-7233     TCGA-HC-7748 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7821     TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5740     TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5745     TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5754     TCGA-CH-5761 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5788 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-CH-5789     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-7115 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7738 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7819     TCGA-HC-7820     TCGA-HI-7168 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171 
"FMN1 WILD-TYPE" "FMN1 WILD-TYPE" "FMN1 WILD-TYPE" 

Clustering(33) Variable = AKT1 MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  AKT1 MUTATED     3   0
  AKT1 WILD-TYPE 485  10
  AKT1 MUTATED AKT1 WILD-TYPE 
             3            495 
  AKT1 MUTATED AKT1 WILD-TYPE 
             0             10 
$`AKT1 MUTATED`
TCGA-EJ-5530 TCGA-J4-A83M TCGA-V1-A8WW 
       60.23        17.85        35.44 

$`AKT1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        64.50        74.93        68.35        61.87        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       62.76        58.45        41.85        60.10        88.34        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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        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-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  AKT1 MUTATED AKT1 WILD-TYPE 
         17.85           0.76 
  AKT1 MUTATED AKT1 WILD-TYPE 
         60.23         165.17 
  AKT1 MUTATED AKT1 WILD-TYPE 
         35.44          30.38 
[1] "17.9 - 60.2 (35.4)" "0.8 - 165.2 (30.4)"
[1] "hr="     "3300000"
D33V2, continuous
                vv
clus              T2  T3  T4
  AKT1 MUTATED     2   1   0
  AKT1 WILD-TYPE 186 292  10
D33V3, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  T2            2            186
  T3            1            292
  T4            0             10
[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"
D33V4, binary
                cls
clus               0   1
  AKT1 MUTATED     2   1
  AKT1 WILD-TYPE 344  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      2    1
  AKT1 WILD-TYPE  344   78
   clus
vv  AKT1 MUTATED AKT1 WILD-TYPE
  0            2            344
  1            1             78
[1] 2 2
[1] FALSE
D33V5, binary
                cls
clus               0   1
  AKT1 MUTATED     2   1
  AKT1 WILD-TYPE 393  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      2    1
  AKT1 WILD-TYPE  393   58
     clus
vv    AKT1 MUTATED AKT1 WILD-TYPE
  NO             2            393
  YES            1             58
[1] 2 2
[1] FALSE
D33V6, binary
                cls
clus               0   1
  AKT1 MUTATED     3   0
  AKT1 WILD-TYPE 480  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  AKT1 MUTATED      3    0
  AKT1 WILD-TYPE  480   15
                                        clus
vv                                       AKT1 MUTATED AKT1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            480
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  AKT1 MUTATED     2   1   0   0
  AKT1 WILD-TYPE 314 146   5  15
D33V7, multiclass
    clus
vv   AKT1 MUTATED AKT1 WILD-TYPE
  R0            2            314
  R1            1            146
  R2            0              5
  RX            0             15
[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"
D33V8, continuous
D33V9, continuous
D33V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AKT1 MUTATED       0                         0     1
  AKT1 WILD-TYPE     2                         7   146
D33V11, multiclass
[1] "Remove cluster labels:" "AKT1 MUTATED"          
clus
  AKT1 MUTATED AKT1 WILD-TYPE 
             1            155 
    TCGA-CH-5753     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5772 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-EJ-5542     TCGA-EJ-7123 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-G9-6364     TCGA-HC-7233     TCGA-HC-7748 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7821     TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5740     TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5745     TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5754     TCGA-CH-5761 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5762     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-5788 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-CH-5789     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-7115     TCGA-EJ-7125 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-G9-6496     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-7736     TCGA-HC-7737     TCGA-HC-7738 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7819     TCGA-HC-7820     TCGA-HI-7168 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171 
"AKT1 WILD-TYPE" "AKT1 WILD-TYPE" "AKT1 WILD-TYPE" 

Clustering(34) Variable = ATM MUTATION ANALYSIS
D34V1, survival
               sevent
clus2             0   1
  ATM MUTATED    21   1
  ATM WILD-TYPE 467   9
  ATM MUTATED ATM WILD-TYPE 
           22           476 
  ATM MUTATED ATM WILD-TYPE 
            1             9 
$`ATM MUTATED`
TCGA-CH-5737 TCGA-CH-5762 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7783 
        2.99        44.02        47.90        48.53        69.63        25.87 
TCGA-EJ-7784 TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-8260 TCGA-HC-A4ZV TCGA-J4-A67Q 
       25.68        38.96        30.97        22.55         0.76        32.05 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-M7-A725 TCGA-V1-A9O7 TCGA-VN-A88K TCGA-XK-AAIW 
       26.43        82.36        18.84        82.16        25.51        40.04 
TCGA-YL-A8S9 TCGA-YL-A8SC TCGA-YL-A8SH TCGA-ZG-A9N3 
       60.56        41.46        28.77        11.47 

$`ATM WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        2.04         0.92        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         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-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       64.60        48.13        62.04        56.98        60.13        60.23 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       62.10        62.10        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        62.76        58.45        60.23        41.85        60.10 
TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       88.34        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-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       35.28        38.37        38.70        36.03        28.24        36.33 
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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7519 TCGA-G9-7522 
       56.75        64.18        50.73        52.93        27.91        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       28.18        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       30.38        17.95        22.32         1.58        15.88        15.55 
TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.94        30.81        27.58        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
        5.85         6.97        10.62        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         2.99         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       67.43        69.27        66.18       113.98        51.25        67.46 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       34.85        25.08        29.23         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
        6.64        63.52        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
        8.84        24.53         6.21        25.18        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ 
       21.80        58.32        42.94        44.88        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19        12.36        37.05        48.03        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA 
        9.04         2.99        31.99        31.96        37.25        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF 
       48.72        75.75        62.14        16.83        56.52        45.14 
TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        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-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  ATM MUTATED ATM WILD-TYPE 
         0.76          0.89 
  ATM MUTATED ATM WILD-TYPE 
        82.36        165.17 
  ATM MUTATED ATM WILD-TYPE 
        31.51         30.38 
[1] "0.8 - 82.4 (31.5)"  "0.9 - 165.2 (30.4)"
[1] "hr=" "2.7"
D34V2, continuous
               vv
clus             T2  T3  T4
  ATM MUTATED     4  17   1
  ATM WILD-TYPE 184 276   9
D34V3, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T2           4           184
  T3          17           276
  T4           1             9
[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"
D34V4, binary
               cls
clus              0   1
  ATM MUTATED    17   4
  ATM WILD-TYPE 329  75
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     17    4
  ATM WILD-TYPE  329   75
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          17           329
  1           4            75
[1] 2 2
[1] FALSE
D34V5, binary
               cls
clus              0   1
  ATM MUTATED    17   2
  ATM WILD-TYPE 378  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     17    2
  ATM WILD-TYPE  378   57
     clus
vv    ATM MUTATED ATM WILD-TYPE
  NO           17           378
  YES           2            57
[1] 2 2
[1] FALSE
D34V6, binary
               cls
clus              0   1
  ATM MUTATED    22   0
  ATM WILD-TYPE 461  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     22    0
  ATM WILD-TYPE  461   15
                                        clus
vv                                       ATM MUTATED ATM WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE             22           461
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE           0            15
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED     9  12   0   0
  ATM WILD-TYPE 307 135   5  15
D34V7, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0           9           307
  R1          12           135
  R2           0             5
  RX           0            15
[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"
D34V8, continuous
D34V9, continuous
D34V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         1     6
  ATM WILD-TYPE     2                         6   141
D34V11, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             6
  WHITE                               6           141
[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(35) Variable = STRC MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  STRC MUTATED     5   0
  STRC WILD-TYPE 483  10
  STRC MUTATED STRC WILD-TYPE 
             5            493 
  STRC MUTATED STRC WILD-TYPE 
             0             10 
$`STRC MUTATED`
TCGA-CH-5753 TCGA-EJ-7318 TCGA-V1-A8WW TCGA-XJ-A83F TCGA-XK-AAIW 
        1.02        33.83        35.44        37.05        40.04 

$`STRC WILD-TYPE`
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5542 
       12.00         1.02        15.98        32.02        33.01        49.74 
TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       84.56        36.13        35.18        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 TCGA-XK-AAK1 
       29.56        32.45         2.73        41.00        41.49        32.19 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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        62.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 
       58.45        60.23        41.85        60.10        88.34        93.70 
TCGA-EJ-7218 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7321 TCGA-EJ-7327 
       83.57        37.81        33.14        25.35        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 
       35.44        28.18        32.68        26.01        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        45.47        32.19        12.36        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  STRC MUTATED STRC WILD-TYPE 
          1.02           0.76 
  STRC MUTATED STRC WILD-TYPE 
         40.04         165.17 
  STRC MUTATED STRC WILD-TYPE 
         35.44          30.38 
[1] "1.0 - 40.0 (35.4)"  "0.8 - 165.2 (30.4)"
[1] "hr="     "3300000"
D35V2, continuous
                vv
clus              T2  T3  T4
  STRC MUTATED     0   5   0
  STRC WILD-TYPE 188 288  10
D35V3, multiclass
    clus
vv   STRC MUTATED STRC WILD-TYPE
  T2            0            188
  T3            5            288
  T4            0             10
[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"
D35V4, binary
                cls
clus               0   1
  STRC MUTATED     2   2
  STRC WILD-TYPE 344  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  STRC MUTATED      2    2
  STRC WILD-TYPE  344   77
   clus
vv  STRC MUTATED STRC WILD-TYPE
  0            2            344
  1            2             77
[1] 2 2
[1] FALSE
D35V5, binary
                cls
clus               0   1
  STRC MUTATED     4   0
  STRC WILD-TYPE 391  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  STRC MUTATED      4    0
  STRC WILD-TYPE  391   59
     clus
vv    STRC MUTATED STRC WILD-TYPE
  NO             4            391
  YES            0             59
[1] 2 2
[1] FALSE
D35V6, binary
                cls
clus               0   1
  STRC MUTATED     5   0
  STRC WILD-TYPE 478  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  STRC MUTATED      5    0
  STRC WILD-TYPE  478   15
                                        clus
vv                                       STRC MUTATED STRC WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               5            478
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            0             15
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  STRC MUTATED     3   1   0   1
  STRC WILD-TYPE 313 146   5  14
D35V7, multiclass
    clus
vv   STRC MUTATED STRC WILD-TYPE
  R0            3            313
  R1            1            146
  R2            0              5
  RX            1             14
[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"
D35V8, continuous
D35V9, continuous
D35V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STRC MUTATED       0                         0     1
  STRC WILD-TYPE     2                         7   146
D35V11, multiclass
[1] "Remove cluster labels:" "STRC MUTATED"          
clus
  STRC MUTATED STRC WILD-TYPE 
             1            155 
    TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5772     TCGA-CH-5790 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5791     TCGA-EJ-5542     TCGA-EJ-7123     TCGA-EJ-7791 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6364     TCGA-HC-7233     TCGA-HC-7748     TCGA-HC-7821 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5788     TCGA-CH-5789 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-7115     TCGA-EJ-7125 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7738 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HC-7818     TCGA-HC-7819     TCGA-HC-7820     TCGA-HI-7168 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171 
"STRC WILD-TYPE" "STRC WILD-TYPE" "STRC WILD-TYPE" 

Clustering(36) Variable = APC MUTATION ANALYSIS
D36V1, survival
               sevent
clus2             0   1
  APC MUTATED     9   1
  APC WILD-TYPE 479   9
  APC MUTATED APC WILD-TYPE 
           10           488 
  APC MUTATED APC WILD-TYPE 
            1             9 
$`APC MUTATED`
TCGA-EJ-7325 TCGA-XK-AAJ3 TCGA-EJ-A8FS TCGA-HC-7819 TCGA-HC-A632 TCGA-HC-A8D0 
       35.18        41.49         8.75        17.85         2.01        25.48 
TCGA-XQ-A8TA TCGA-YL-A8S8 TCGA-YL-A8SO TCGA-YL-A9WI 
        4.80        62.14       114.38        53.36 

$`APC WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7791 TCGA-EJ-A46B TCGA-EJ-A46G 
       49.74        84.56        36.13        36.76        21.60        21.96 
TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 TCGA-HC-7821 
       14.83        28.70        39.39        44.55        26.04        31.43 
TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA TCGA-KK-A7AP 
        3.48         7.00        32.61        40.67        19.66         6.44 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAK1 TCGA-2A-A8VL 
       29.56        32.45         2.73        41.00        32.19        20.42 
TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       55.92        45.14        22.06        45.30         3.68        28.37 
TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 TCGA-CH-5738 
       44.84        41.82        20.22        11.51         2.99         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
       22.06         1.02        12.99        13.97         1.97         2.99 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5754 
       24.03         1.02        13.02        35.01        31.00         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
        0.92        44.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         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        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        45.30        44.81        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       28.18        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7820 
       23.80        17.16        25.71        30.51        30.84        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
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        15.55 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
       22.36         0.76         1.78         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM 
        5.85         6.97        10.62        10.55        13.32        15.22 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         2.99         8.65         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       83.34        64.70        86.40        81.17       141.21        48.76 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       72.26       165.17        67.59       115.13        68.15       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       90.74        58.19        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TB TCGA-Y6-A8TL 
       41.39        36.95        47.15        51.81        25.32        32.61 
TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       17.29         4.87        52.96        49.02        51.45        48.72 
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-A8SH TCGA-YL-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP 
       28.77        53.06        45.86        46.29        32.45        77.79 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-YL-A9WL 
       68.48         8.98        14.04        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  APC MUTATED APC WILD-TYPE 
         2.01          0.76 
  APC MUTATED APC WILD-TYPE 
       114.38        165.17 
  APC MUTATED APC WILD-TYPE 
       30.330        30.445 
[1] "2.0 - 114.4 (30.3)" "0.8 - 165.2 (30.4)"
[1] "hr=" "4"  
D36V2, continuous
               vv
clus             T2  T3  T4
  APC MUTATED     2   7   0
  APC WILD-TYPE 186 286  10
D36V3, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T2           2           186
  T3           7           286
  T4           0            10
[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"
D36V4, binary
               cls
clus              0   1
  APC MUTATED     7   1
  APC WILD-TYPE 339  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      7    1
  APC WILD-TYPE  339   78
   clus
vv  APC MUTATED APC WILD-TYPE
  0           7           339
  1           1            78
[1] 2 2
[1] FALSE
D36V5, binary
               cls
clus              0   1
  APC MUTATED     9   0
  APC WILD-TYPE 386  59
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      9    0
  APC WILD-TYPE  386   59
     clus
vv    APC MUTATED APC WILD-TYPE
  NO            9           386
  YES           0            59
[1] 2 2
[1] FALSE
D36V6, binary
               cls
clus              0   1
  APC MUTATED    10   0
  APC WILD-TYPE 473  15
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     10    0
  APC WILD-TYPE  473   15
                                        clus
vv                                       APC MUTATED APC WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE             10           473
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE           0            15
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED     6   2   1   0
  APC WILD-TYPE 310 145   4  15
D36V7, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0           6           310
  R1           2           145
  R2           1             4
  RX           0            15
[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"
D36V8, continuous
D36V9, continuous
D36V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED       0                         0     1
  APC WILD-TYPE     2                         7   146
D36V11, multiclass
[1] "Remove cluster labels:" "APC MUTATED"           
clus
  APC MUTATED APC WILD-TYPE 
            1           155 
   TCGA-CH-5753    TCGA-CH-5763    TCGA-CH-5764    TCGA-CH-5772    TCGA-CH-5790 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5791    TCGA-EJ-5542    TCGA-EJ-7123    TCGA-EJ-7791    TCGA-G9-6364 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7233    TCGA-HC-7748    TCGA-HC-7821    TCGA-CH-5737    TCGA-CH-5738 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5739    TCGA-CH-5740    TCGA-CH-5741    TCGA-CH-5743    TCGA-CH-5744 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5745    TCGA-CH-5746    TCGA-CH-5748    TCGA-CH-5750    TCGA-CH-5751 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5752    TCGA-CH-5754    TCGA-CH-5761    TCGA-CH-5762    TCGA-CH-5765 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5766    TCGA-CH-5767    TCGA-CH-5768    TCGA-CH-5769    TCGA-CH-5771 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5788    TCGA-CH-5789    TCGA-CH-5792    TCGA-CH-5794    TCGA-EJ-5494 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5495    TCGA-EJ-5496    TCGA-EJ-5497    TCGA-EJ-5498    TCGA-EJ-5499 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5501    TCGA-EJ-5503    TCGA-EJ-5504    TCGA-EJ-5505    TCGA-EJ-5506 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5507    TCGA-EJ-5508    TCGA-EJ-5509    TCGA-EJ-5510    TCGA-EJ-5511 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5512    TCGA-EJ-5514    TCGA-EJ-5515    TCGA-EJ-5516    TCGA-EJ-5517 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5518    TCGA-EJ-5519    TCGA-EJ-5521    TCGA-EJ-5522    TCGA-EJ-5524 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5525    TCGA-EJ-5526    TCGA-EJ-5527    TCGA-EJ-5530    TCGA-EJ-5531 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5532    TCGA-EJ-7115    TCGA-EJ-7125    TCGA-EJ-7314    TCGA-EJ-7315 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7317    TCGA-EJ-7321    TCGA-EJ-7327    TCGA-EJ-7328    TCGA-EJ-7330 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7331    TCGA-EJ-7781    TCGA-EJ-7782    TCGA-EJ-7783    TCGA-EJ-7784 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7785    TCGA-EJ-7786    TCGA-EJ-7788    TCGA-EJ-7789    TCGA-EJ-7792 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7793    TCGA-EJ-7794    TCGA-EJ-7797    TCGA-FC-7708    TCGA-FC-7961 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6329    TCGA-G9-6332    TCGA-G9-6333    TCGA-G9-6336    TCGA-G9-6338 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6342    TCGA-G9-6343    TCGA-G9-6348    TCGA-G9-6351    TCGA-G9-6353 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6356    TCGA-G9-6361    TCGA-G9-6362    TCGA-G9-6363    TCGA-G9-6365 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6366    TCGA-G9-6367    TCGA-G9-6369    TCGA-G9-6370    TCGA-G9-6371 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6373    TCGA-G9-6377    TCGA-G9-6378    TCGA-G9-6384    TCGA-G9-6385 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6494    TCGA-G9-6496    TCGA-G9-6499    TCGA-H9-7775    TCGA-HC-7075 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7077    TCGA-HC-7078    TCGA-HC-7079    TCGA-HC-7080    TCGA-HC-7081 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7209    TCGA-HC-7210    TCGA-HC-7211    TCGA-HC-7212    TCGA-HC-7213 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7230    TCGA-HC-7231    TCGA-HC-7232    TCGA-HC-7736    TCGA-HC-7737 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7738    TCGA-HC-7740    TCGA-HC-7742    TCGA-HC-7744    TCGA-HC-7745 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7747    TCGA-HC-7749    TCGA-HC-7750    TCGA-HC-7752    TCGA-HC-7818 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7820    TCGA-HI-7168    TCGA-HI-7169    TCGA-HI-7170    TCGA-HI-7171 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 

Clustering(37) Variable = ZFP36L2 MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                 0   1
  ZFP36L2 MUTATED     3   1
  ZFP36L2 WILD-TYPE 485   9
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                4               494 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                1                 9 
$`ZFP36L2 MUTATED`
TCGA-EJ-7783 TCGA-G9-A9S0 TCGA-KK-A7AZ TCGA-XK-AAIW 
       25.87        26.01        49.94        40.04 

$`ZFP36L2 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       38.37        25.68        38.70        36.03        28.24        36.33 
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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S4 TCGA-G9-A9S7 
       30.97        35.44        28.18        32.68        29.79        23.93 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 
        6.08        30.94         3.68        19.76        69.53        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       38.93        36.36        37.35        14.47        28.54        40.14 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 
       28.60        40.08        32.91        30.87        38.17        36.26 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
       35.84        31.69        23.57        30.84        17.46        23.70 
TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        23.80        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7B0 
       52.93        58.36        27.02        34.65        57.67        43.69 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       34.95        36.13        74.27       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       62.96        16.21        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN 
       25.08        29.23        18.84         5.69         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            25.87              0.76 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
            49.94            165.17 
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
           33.025            30.445 
[1] "25.9 - 49.9 (33.0)" "0.8 - 165.2 (30.4)"
[1] "hr=" "21" 
D37V2, continuous
                   vv
clus                 T2  T3  T4
  ZFP36L2 MUTATED     0   4   0
  ZFP36L2 WILD-TYPE 188 289  10
D37V3, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  T2               0               188
  T3               4               289
  T4               0                10
[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"
D37V4, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     3   1
  ZFP36L2 WILD-TYPE 343  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      3    1
  ZFP36L2 WILD-TYPE  343   78
   clus
vv  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  0               3               343
  1               1                78
[1] 2 2
[1] FALSE
D37V5, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     2   1
  ZFP36L2 WILD-TYPE 393  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      2    1
  ZFP36L2 WILD-TYPE  393   58
     clus
vv    ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  NO                2               393
  YES               1                58
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                  0   1
  ZFP36L2 MUTATED     4   0
  ZFP36L2 WILD-TYPE 479  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFP36L2 MUTATED      4    0
  ZFP36L2 WILD-TYPE  479   15
                                        clus
vv                                       ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE               0                15
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  ZFP36L2 MUTATED     2   2   0   0
  ZFP36L2 WILD-TYPE 314 145   5  15
D37V7, multiclass
    clus
vv   ZFP36L2 MUTATED ZFP36L2 WILD-TYPE
  R0               2               314
  R1               2               145
  R2               0                 5
  RX               0                15
[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"
D37V8, continuous
D37V9, continuous
D37V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFP36L2 MUTATED       0                         0     1
  ZFP36L2 WILD-TYPE     2                         7   146
D37V11, multiclass
[1] "Remove cluster labels:" "ZFP36L2 MUTATED"       
clus
  ZFP36L2 MUTATED ZFP36L2 WILD-TYPE 
                1               155 
       TCGA-CH-5753        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5772 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-EJ-5542        TCGA-EJ-7123 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7791        TCGA-G9-6364        TCGA-HC-7233        TCGA-HC-7748 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7821        TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5745        TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5754        TCGA-CH-5761 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5788 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-7115 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7321        TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7331        TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7784 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7738 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7747        TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HC-7818        TCGA-HC-7819        TCGA-HC-7820        TCGA-HI-7168 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" "ZFP36L2 WILD-TYPE" 

Clustering(38) Variable = MYOT MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  MYOT MUTATED     5   0
  MYOT WILD-TYPE 483  10
  MYOT MUTATED MYOT WILD-TYPE 
             5            493 
  MYOT MUTATED MYOT WILD-TYPE 
             0             10 
$`MYOT MUTATED`
TCGA-J9-A52D TCGA-KK-A59V TCGA-V1-A8WL TCGA-XK-AAIW TCGA-ZG-A8QY 
        6.97       113.10        64.04        40.04        13.28 

$`MYOT WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       69.53        65.26        38.93        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        40.14        28.60        40.08        32.91        30.87 
TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       38.17        36.26        35.84        31.69        23.57        30.84 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       17.46        23.70        24.59        23.80        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 
       30.51        30.84        17.85        24.56        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87        27.85        30.38        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        15.55        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.45         1.25         4.41         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
       18.84        19.30        27.75       109.25        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        40.04        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       30.81        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B 
       23.67        17.85        18.18        13.55        27.12        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        5.85        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        2.99         8.65         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW 
       39.29        61.68        30.38        15.58        22.55        35.44 
TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       37.25        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       49.91        36.10         3.09        14.53        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU 
       20.28        19.17        12.43         3.78        16.96        19.04 
TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND 
       12.16        22.75        17.98        14.96        11.47        13.48 
TCGA-ZG-A9NI 
        4.34 

  MYOT MUTATED MYOT WILD-TYPE 
          6.97           0.76 
  MYOT MUTATED MYOT WILD-TYPE 
        113.10         165.17 
  MYOT MUTATED MYOT WILD-TYPE 
         40.04          30.38 
[1] "7.0 - 113.1 (40.0)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9200000"
D38V2, continuous
                vv
clus              T2  T3  T4
  MYOT MUTATED     0   5   0
  MYOT WILD-TYPE 188 288  10
D38V3, multiclass
    clus
vv   MYOT MUTATED MYOT WILD-TYPE
  T2            0            188
  T3            5            288
  T4            0             10
[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"
D38V4, binary
                cls
clus               0   1
  MYOT MUTATED     3   1
  MYOT WILD-TYPE 343  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOT MUTATED      3    1
  MYOT WILD-TYPE  343   78
   clus
vv  MYOT MUTATED MYOT WILD-TYPE
  0            3            343
  1            1             78
[1] 2 2
[1] FALSE
D38V5, binary
                cls
clus               0   1
  MYOT MUTATED     5   0
  MYOT WILD-TYPE 390  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOT MUTATED      5    0
  MYOT WILD-TYPE  390   59
     clus
vv    MYOT MUTATED MYOT WILD-TYPE
  NO             5            390
  YES            0             59
[1] 2 2
[1] FALSE
D38V6, binary
                cls
clus               0   1
  MYOT MUTATED     4   1
  MYOT WILD-TYPE 479  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOT MUTATED      4    1
  MYOT WILD-TYPE  479   14
                                        clus
vv                                       MYOT MUTATED MYOT WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               4            479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            1             14
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYOT MUTATED     3   1   0   1
  MYOT WILD-TYPE 313 146   5  14
D38V7, multiclass
    clus
vv   MYOT MUTATED MYOT WILD-TYPE
  R0            3            313
  R1            1            146
  R2            0              5
  RX            1             14
[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"
D38V8, continuous
D38V9, continuous
D38V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYOT MUTATED       0                         0     0
  MYOT WILD-TYPE     2                         7   147
D38V11, multiclass

Clustering(39) Variable = KIRREL MUTATION ANALYSIS
D39V1, survival
                  sevent
clus2                0   1
  KIRREL MUTATED     6   0
  KIRREL WILD-TYPE 482  10
  KIRREL MUTATED KIRREL WILD-TYPE 
               6              492 
  KIRREL MUTATED KIRREL WILD-TYPE 
               0               10 
$`KIRREL MUTATED`
TCGA-XK-AAK1 TCGA-EJ-5515 TCGA-EJ-5519 TCGA-G9-6353 TCGA-HC-8262 TCGA-KK-A7AQ 
       32.19        60.23        64.50        50.70        22.32        52.93 

$`KIRREL WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        55.92        45.14        22.06        45.30         3.68 
TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
       28.37        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 
       56.98        60.13        62.10        62.10        69.63        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        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        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-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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       68.68        49.81        67.33        67.92        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        44.81        64.01        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       52.93        38.96        27.91        30.97        35.44        28.18 
TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX 
       32.68        26.01        29.79        23.93         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
        3.68        19.76        69.53        65.26        38.93        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        40.14        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
       32.91        30.87        38.17        36.26        35.84        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 
       23.57        30.84        17.46        23.70        24.59        23.80 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87        27.85        30.38 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       22.55        17.95         1.58        15.88        15.55        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY 
        2.33         1.45         1.25         4.41         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 
       25.48        18.84        19.30        27.75       109.25        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        40.04        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        30.81        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 
       10.78        23.67        17.85        18.18        13.55        27.12 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL 
       13.87         5.85         6.97        10.62        10.55        13.32 
TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       15.22        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE 
       43.66        21.86         2.99         8.65         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        83.34        64.70        86.40        81.17       141.21 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       48.76        72.26       165.17        67.59       115.13        68.15 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
      113.33        90.74        58.19        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 
       57.67        49.94        43.69        34.95        36.13        74.27 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        67.46        20.65        62.96        16.21        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        5.69         3.19       140.19       122.17        86.14        18.12 
TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
        0.89        17.29        20.05        47.64        28.18        58.88 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        61.68        64.04        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 
       15.58        22.55        35.44         6.64        63.52        82.16 
TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ 
       94.36        20.91        38.93        79.00        62.89        12.20 
TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 
       15.65        37.28        35.08        28.73        27.19        17.75 
TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K 
       49.87        53.92        45.47        44.75         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        25.18        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       58.32        42.94        44.88        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       12.36        37.05        48.03        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA 
        2.99        31.99        31.96        37.25        40.04        30.58 
TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB 
       41.39        36.95        47.15        51.81         4.80        25.32 
TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK 
       41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY 
       53.36        60.99        70.22        24.33        49.91        36.10 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 
        3.09        14.53        13.28        10.13         4.27        11.67 
TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 
       42.81        37.94        36.43        29.85        22.59        20.28 
TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       19.17        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  KIRREL MUTATED KIRREL WILD-TYPE 
           22.32             0.76 
  KIRREL MUTATED KIRREL WILD-TYPE 
           64.50           165.17 
  KIRREL MUTATED KIRREL WILD-TYPE 
          51.815           30.365 
[1] "22.3 - 64.5 (51.8)" "0.8 - 165.2 (30.4)"
[1] "hr="     "9100000"
D39V2, continuous
                  vv
clus                T2  T3  T4
  KIRREL MUTATED     3   3   0
  KIRREL WILD-TYPE 185 290  10
D39V3, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  T2              3              185
  T3              3              290
  T4              0               10
[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"
D39V4, binary
                  cls
clus                 0   1
  KIRREL MUTATED     4   1
  KIRREL WILD-TYPE 342  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      4    1
  KIRREL WILD-TYPE  342   78
   clus
vv  KIRREL MUTATED KIRREL WILD-TYPE
  0              4              342
  1              1               78
[1] 2 2
[1] FALSE
D39V5, binary
                  cls
clus                 0   1
  KIRREL MUTATED     6   0
  KIRREL WILD-TYPE 389  59
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      6    0
  KIRREL WILD-TYPE  389   59
     clus
vv    KIRREL MUTATED KIRREL WILD-TYPE
  NO               6              389
  YES              0               59
[1] 2 2
[1] FALSE
D39V6, binary
                  cls
clus                 0   1
  KIRREL MUTATED     6   0
  KIRREL WILD-TYPE 477  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      6    0
  KIRREL WILD-TYPE  477   15
                                        clus
vv                                       KIRREL MUTATED KIRREL WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 6              477
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE              0               15
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIRREL MUTATED     5   1   0   0
  KIRREL WILD-TYPE 311 146   5  15
D39V7, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  R0              5              311
  R1              1              146
  R2              0                5
  RX              0               15
[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"
D39V8, continuous
D39V9, continuous
D39V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIRREL MUTATED       0                         0     3
  KIRREL WILD-TYPE     2                         7   144
D39V11, multiclass
                           clus
vv                          KIRREL MUTATED KIRREL WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[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(40) Variable = PGBD2 MUTATION ANALYSIS
D40V1, survival
                 sevent
clus2               0   1
  PGBD2 MUTATED     3   0
  PGBD2 WILD-TYPE 485  10
  PGBD2 MUTATED PGBD2 WILD-TYPE 
              3             495 
  PGBD2 MUTATED PGBD2 WILD-TYPE 
              0              10 
$`PGBD2 MUTATED`
TCGA-EJ-7782 TCGA-KK-A59V TCGA-XK-AAIW 
       38.37       113.10        40.04 

$`PGBD2 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-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-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-A46E TCGA-EJ-A46F 
       38.10        24.85        25.18        20.58        17.23        25.74 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        6.97        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        2.99         8.65         8.88        11.57        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       25.18        15.81        41.42        44.91        25.78        16.31 
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-VP-AA1N TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       44.88        14.76        45.47        32.19        12.36        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       48.03        42.08        48.03         9.04         2.99        31.99 
TCGA-XK-AAIR TCGA-XK-AAIV TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       31.96        37.25        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        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-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  PGBD2 MUTATED PGBD2 WILD-TYPE 
          38.37            0.76 
  PGBD2 MUTATED PGBD2 WILD-TYPE 
         113.10          165.17 
  PGBD2 MUTATED PGBD2 WILD-TYPE 
          40.04           30.38 
[1] "38.4 - 113.1 (40.0)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "9100000"
D40V2, continuous
                 vv
clus               T2  T3  T4
  PGBD2 MUTATED     1   2   0
  PGBD2 WILD-TYPE 187 291  10
D40V3, multiclass
    clus
vv   PGBD2 MUTATED PGBD2 WILD-TYPE
  T2             1             187
  T3             2             291
  T4             0              10
[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"
D40V4, binary
                 cls
clus                0   1
  PGBD2 MUTATED     3   0
  PGBD2 WILD-TYPE 343  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD2 MUTATED      3    0
  PGBD2 WILD-TYPE  343   79
   clus
vv  PGBD2 MUTATED PGBD2 WILD-TYPE
  0             3             343
  1             0              79
[1] 2 2
[1] FALSE
D40V5, binary
                 cls
clus                0   1
  PGBD2 MUTATED     3   0
  PGBD2 WILD-TYPE 392  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD2 MUTATED      3    0
  PGBD2 WILD-TYPE  392   59
     clus
vv    PGBD2 MUTATED PGBD2 WILD-TYPE
  NO              3             392
  YES             0              59
[1] 2 2
[1] FALSE
D40V6, binary
                 cls
clus                0   1
  PGBD2 MUTATED     3   0
  PGBD2 WILD-TYPE 480  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PGBD2 MUTATED      3    0
  PGBD2 WILD-TYPE  480   15
                                        clus
vv                                       PGBD2 MUTATED PGBD2 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             480
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PGBD2 MUTATED     2   1   0   0
  PGBD2 WILD-TYPE 314 146   5  15
D40V7, multiclass
    clus
vv   PGBD2 MUTATED PGBD2 WILD-TYPE
  R0             2             314
  R1             1             146
  R2             0               5
  RX             0              15
[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"
D40V8, continuous
D40V9, continuous
D40V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PGBD2 MUTATED       0                         1     0
  PGBD2 WILD-TYPE     2                         6   147
D40V11, multiclass
[1] "Remove cluster labels:" "PGBD2 MUTATED"         
clus
  PGBD2 MUTATED PGBD2 WILD-TYPE 
              1             155 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7783      TCGA-EJ-7784 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7747      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" "PGBD2 WILD-TYPE" 

Clustering(41) Variable = LOC100132247 MUTATION ANALYSIS
D41V1, survival
                        sevent
clus2                      0   1
  LOC100132247 MUTATED     3   0
  LOC100132247 WILD-TYPE 485  10
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                     3                    495 
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                     0                     10 
$`LOC100132247 MUTATED`
TCGA-EJ-A65E TCGA-KC-A4BL TCGA-MG-AAMC 
       13.71        30.71         5.69 

$`LOC100132247 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65F 
       25.74        23.80        21.96        23.34        12.92        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       21.90         7.56        11.61         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 
        9.83         8.75         4.54         4.31         4.77        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        28.83        22.36        17.23        25.94        20.25 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        80.55        68.68        49.81        67.33        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 
       67.92        47.15        46.52        47.44        45.30        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       64.01        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 
       56.75        64.18        50.73        52.93        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 
       30.97        35.44        28.18        32.68        26.01        29.79 
TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 
       23.93         6.08        30.94         3.68        19.76        69.53 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       23.70        24.59        23.80        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        24.56        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87        27.85        30.38        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        15.55        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HC-A9TE TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       19.30        27.75       109.25        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        40.04        33.01        25.32        30.94        30.81 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C 
       17.85        18.18        13.55        27.12        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP 
        6.97        10.62        10.55        13.32        15.22        12.69 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN 
       34.85        25.08        29.23        18.84         3.19       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV 
      122.17        86.14        18.12         0.89        17.29        20.05 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       47.64        28.18        58.88        16.70        14.73        39.29 
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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF 
        6.64        63.52        82.16        94.36        20.91        38.93 
TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY 
       79.00        62.89        12.20        15.65        37.28        35.08 
TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK 
       28.73        27.19        17.75        49.87        53.92        45.47 
TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       44.75         8.84        25.51        24.53         6.21        25.18 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 
       15.81        41.42        44.91        25.78        16.31       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-VP-AA1N 
       60.92        66.97        21.80        58.32        42.94        44.88 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19        12.36        37.05        48.03 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR 
       42.08        48.03         9.04         2.99        31.99        31.96 
TCGA-XK-AAIV TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT 
       37.25        40.04        30.58        41.39        36.95        47.15 
TCGA-XK-AAJU TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW 
       51.81         4.80        25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       53.06        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-YL-A9WK 
       68.48         8.98        14.04        53.36        60.99        70.22 
TCGA-YL-A9WL TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       24.33        49.91        36.10         3.09        14.53        13.28 
TCGA-ZG-A8QZ TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 
       10.13         4.27        11.67        42.81        37.94        36.43 
TCGA-ZG-A9L5 TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN 
       29.85        22.59        20.28        19.17        12.43         3.78 
TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC 
       16.96        19.04        12.16        22.75        17.98        14.96 
TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       11.47        13.48         4.34 

  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                  5.69                   0.76 
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                 30.71                 165.17 
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                 13.71                  30.51 
[1] "5.7 - 30.7 (13.7)"  "0.8 - 165.2 (30.5)"
[1] "hr="     "1200000"
D41V2, continuous
                        vv
clus                      T2  T3  T4
  LOC100132247 MUTATED     1   2   0
  LOC100132247 WILD-TYPE 187 291  10
D41V3, multiclass
    clus
vv   LOC100132247 MUTATED LOC100132247 WILD-TYPE
  T2                    1                    187
  T3                    2                    291
  T4                    0                     10
[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"
D41V4, binary
                        cls
clus                       0   1
  LOC100132247 MUTATED     3   0
  LOC100132247 WILD-TYPE 343  79
[1] "tbl2"
                        cls
clus                     [,1] [,2]
  LOC100132247 MUTATED      3    0
  LOC100132247 WILD-TYPE  343   79
   clus
vv  LOC100132247 MUTATED LOC100132247 WILD-TYPE
  0                    3                    343
  1                    0                     79
[1] 2 2
[1] FALSE
D41V5, binary
                        cls
clus                       0   1
  LOC100132247 MUTATED     2   0
  LOC100132247 WILD-TYPE 393  59
[1] "tbl2"
                        cls
clus                     [,1] [,2]
  LOC100132247 MUTATED      2    0
  LOC100132247 WILD-TYPE  393   59
     clus
vv    LOC100132247 MUTATED LOC100132247 WILD-TYPE
  NO                     2                    393
  YES                    0                     59
[1] 2 2
[1] FALSE
D41V6, binary
                        cls
clus                       0   1
  LOC100132247 MUTATED     2   1
  LOC100132247 WILD-TYPE 481  14
[1] "tbl2"
                        cls
clus                     [,1] [,2]
  LOC100132247 MUTATED      2    1
  LOC100132247 WILD-TYPE  481   14
                                        clus
vv                                       LOC100132247 MUTATED
  PROSTATE ADENOCARCINOMA ACINAR TYPE                       2
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                    1
                                        clus
vv                                       LOC100132247 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                       481
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE                     14
[1] 2 2
[1] FALSE
                        vv
clus                      R0  R1  R2  RX
  LOC100132247 MUTATED     3   0   0   0
  LOC100132247 WILD-TYPE 313 147   5  15
D41V7, multiclass
    clus
vv   LOC100132247 MUTATED LOC100132247 WILD-TYPE
  R0                    3                    313
  R1                    0                    147
  R2                    0                      5
  RX                    0                     15
[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"
D41V8, continuous
[1] "Remove cluster labels:" "LOC100132247 MUTATED"  
clus
  LOC100132247 MUTATED LOC100132247 WILD-TYPE 
                     2                    405 
            TCGA-CH-5753             TCGA-CH-5763             TCGA-CH-5764 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5772             TCGA-CH-5790             TCGA-CH-5791 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5542             TCGA-EJ-7123             TCGA-EJ-7312 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7325             TCGA-EJ-7791             TCGA-EJ-A46B 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A46G             TCGA-EJ-A65J             TCGA-EJ-A6RC 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6364             TCGA-HC-7233             TCGA-HC-7748 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7821             TCGA-HC-A76W             TCGA-KC-A7FA 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A7AP             TCGA-KK-A7B3             TCGA-KK-A7B4 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-QU-A6IM             TCGA-XK-AAJ3             TCGA-XK-AAK1 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-2A-A8VL             TCGA-2A-A8VT             TCGA-2A-A8VV 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-2A-A8VX             TCGA-2A-A8W1             TCGA-2A-A8W3 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-2A-AAYU             TCGA-4L-AA1F             TCGA-CH-5737 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5739             TCGA-CH-5740             TCGA-CH-5741 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5743             TCGA-CH-5744             TCGA-CH-5745 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5746             TCGA-CH-5748             TCGA-CH-5750 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5751             TCGA-CH-5752             TCGA-CH-5754 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5761             TCGA-CH-5762             TCGA-CH-5765 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5766             TCGA-CH-5767             TCGA-CH-5768 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5769             TCGA-CH-5771             TCGA-CH-5788 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-CH-5789             TCGA-CH-5792             TCGA-CH-5794 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5494             TCGA-EJ-5495             TCGA-EJ-5496 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5497             TCGA-EJ-5498             TCGA-EJ-5499 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5501             TCGA-EJ-5502             TCGA-EJ-5503 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5504             TCGA-EJ-5505             TCGA-EJ-5506 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5507             TCGA-EJ-5508             TCGA-EJ-5509 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5510             TCGA-EJ-5511             TCGA-EJ-5512 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5514             TCGA-EJ-5515             TCGA-EJ-5516 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5517             TCGA-EJ-5518             TCGA-EJ-5519 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5521             TCGA-EJ-5522             TCGA-EJ-5524 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5525             TCGA-EJ-5526             TCGA-EJ-5527 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-5530             TCGA-EJ-5531             TCGA-EJ-5532 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7115             TCGA-EJ-7125             TCGA-EJ-7218 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7314             TCGA-EJ-7315             TCGA-EJ-7317 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7321             TCGA-EJ-7327             TCGA-EJ-7328 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7330             TCGA-EJ-7331             TCGA-EJ-7781 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7782             TCGA-EJ-7783             TCGA-EJ-7784 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7785             TCGA-EJ-7786             TCGA-EJ-7788 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7789             TCGA-EJ-7792             TCGA-EJ-7794 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-7797             TCGA-EJ-8468             TCGA-EJ-8469 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-8470             TCGA-EJ-8472             TCGA-EJ-8474 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A46D             TCGA-EJ-A46E             TCGA-EJ-A46F 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A65B             TCGA-EJ-A65D             TCGA-EJ-A65F 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A65G             TCGA-EJ-A65M             TCGA-EJ-A6RA 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A7NF             TCGA-EJ-A7NG             TCGA-EJ-A7NJ 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A7NK             TCGA-EJ-A7NM             TCGA-EJ-A7NN 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A8FN             TCGA-EJ-A8FO             TCGA-EJ-A8FP 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-A8FS             TCGA-EJ-A8FU             TCGA-EJ-AB20 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-EJ-AB27             TCGA-FC-7708             TCGA-FC-7961 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-FC-A5OB             TCGA-FC-A66V             TCGA-FC-A6HD 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-FC-A8O0             TCGA-G9-6332             TCGA-G9-6333 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6336             TCGA-G9-6338             TCGA-G9-6339 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6348             TCGA-G9-6356             TCGA-G9-6361 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6362             TCGA-G9-6363             TCGA-G9-6365 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6367             TCGA-G9-6369             TCGA-G9-6370 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6377             TCGA-G9-6379             TCGA-G9-6384 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-6494             TCGA-G9-6496             TCGA-G9-6499 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-7510             TCGA-G9-7521             TCGA-G9-7522 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-7523             TCGA-G9-7525             TCGA-G9-A9S0 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-G9-A9S4             TCGA-G9-A9S7             TCGA-H9-A6BY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7078             TCGA-HC-7079             TCGA-HC-7080 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7209             TCGA-HC-7210             TCGA-HC-7211 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7212             TCGA-HC-7213             TCGA-HC-7230 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7736             TCGA-HC-7737             TCGA-HC-7740 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7742             TCGA-HC-7744             TCGA-HC-7745 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7747             TCGA-HC-7749             TCGA-HC-7752 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-7818             TCGA-HC-7819             TCGA-HC-8216 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-8257             TCGA-HC-8258             TCGA-HC-8260 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-8262             TCGA-HC-8264             TCGA-HC-8265 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-8266             TCGA-HC-A48F             TCGA-HC-A4ZV 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-A631             TCGA-HC-A632             TCGA-HC-A6AL 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-A6AN             TCGA-HC-A6AS             TCGA-HC-A6HX 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-A76X             TCGA-HC-A8CY             TCGA-HC-A8D0 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HC-A8D1             TCGA-HC-A9TE             TCGA-HC-A9TH 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HI-7168             TCGA-HI-7169             TCGA-HI-7170 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-HI-7171             TCGA-J4-8200             TCGA-J4-A67L 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J4-A67M             TCGA-J4-A67N             TCGA-J4-A67O 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J4-A67R             TCGA-J4-A67S             TCGA-J4-A6G1 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J4-A6G3             TCGA-J4-A83I             TCGA-J4-A83J 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J4-A83L             TCGA-J4-A83M             TCGA-J4-AATZ 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J4-AAU2             TCGA-J9-A52B             TCGA-J9-A52E 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-J9-A8CM             TCGA-KC-A4BN             TCGA-KC-A4BO 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KC-A4BR             TCGA-KC-A4BV             TCGA-KC-A7F3 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KC-A7F5             TCGA-KC-A7F6             TCGA-KC-A7FD 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KC-A7FE             TCGA-KK-A59V             TCGA-KK-A59X 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A59Y             TCGA-KK-A59Z             TCGA-KK-A5A1 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A6DY             TCGA-KK-A6E0             TCGA-KK-A6E1 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A6E2             TCGA-KK-A6E3             TCGA-KK-A6E4 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A6E5             TCGA-KK-A6E6             TCGA-KK-A6E7 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A6E8             TCGA-KK-A7AQ             TCGA-KK-A7AU 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A7AV             TCGA-KK-A7AW             TCGA-KK-A7AY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A7AZ             TCGA-KK-A7B0             TCGA-KK-A7B1 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A7B2             TCGA-KK-A8I4             TCGA-KK-A8I6 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A8I7             TCGA-KK-A8IA             TCGA-KK-A8ID 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-KK-A8IJ             TCGA-KK-A8IL             TCGA-M7-A71Z 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-M7-A722             TCGA-M7-A723             TCGA-M7-A724 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-M7-A725             TCGA-QU-A6IL             TCGA-QU-A6IN 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-QU-A6IO             TCGA-QU-A6IP             TCGA-SU-A7E7 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-TP-A8TT             TCGA-TP-A8TV             TCGA-V1-A8MF 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A8MJ             TCGA-V1-A8ML             TCGA-V1-A8MM 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A8MU             TCGA-V1-A8WL             TCGA-V1-A8WV 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A8WW             TCGA-V1-A8X3             TCGA-V1-A9O5 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A9O7             TCGA-V1-A9O9             TCGA-V1-A9OA 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A9OL             TCGA-V1-A9OX             TCGA-V1-A9OY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A9Z7             TCGA-V1-A9Z8             TCGA-V1-A9Z9 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-V1-A9ZG             TCGA-V1-A9ZI             TCGA-V1-A9ZK 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VN-A88I             TCGA-VN-A88K             TCGA-VN-A88L 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VN-A88M             TCGA-VN-A88N             TCGA-VN-A88O 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VN-A88P             TCGA-VN-A88Q             TCGA-VN-A88R 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VN-A943             TCGA-VP-A872             TCGA-VP-A875 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VP-A876             TCGA-VP-A878             TCGA-VP-A879 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VP-A87B             TCGA-VP-A87C             TCGA-VP-A87D 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VP-A87E             TCGA-VP-A87H             TCGA-VP-A87J 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-VP-A87K             TCGA-VP-AA1N             TCGA-WW-A8ZI 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-X4-A8KQ             TCGA-XA-A8JR             TCGA-XJ-A83F 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-XJ-A83G             TCGA-XJ-A9DI             TCGA-XJ-A9DX 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-XK-AAIR             TCGA-XK-AAIV             TCGA-XK-AAIW 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-XK-AAJA             TCGA-XK-AAJP             TCGA-XK-AAJR 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-XK-AAJT             TCGA-XK-AAJU             TCGA-XQ-A8TB 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-Y6-A8TL             TCGA-Y6-A9XI             TCGA-YJ-A8SW 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8HK             TCGA-YL-A8HL             TCGA-YL-A8HM 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8HO             TCGA-YL-A8S8             TCGA-YL-A8S9 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8SA             TCGA-YL-A8SB             TCGA-YL-A8SC 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8SF             TCGA-YL-A8SH             TCGA-YL-A8SI 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8SJ             TCGA-YL-A8SK             TCGA-YL-A8SL 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A8SQ             TCGA-YL-A8SR             TCGA-YL-A9WH 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A9WI             TCGA-YL-A9WJ             TCGA-YL-A9WK 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-YL-A9WL             TCGA-YL-A9WX             TCGA-YL-A9WY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A8QW             TCGA-ZG-A8QX             TCGA-ZG-A8QY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A8QZ             TCGA-ZG-A9KY             TCGA-ZG-A9L0 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9L1             TCGA-ZG-A9L2             TCGA-ZG-A9L4 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9L5             TCGA-ZG-A9L6             TCGA-ZG-A9L9 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9LB             TCGA-ZG-A9LM             TCGA-ZG-A9LN 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9LS             TCGA-ZG-A9LU             TCGA-ZG-A9LY 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9LZ             TCGA-ZG-A9M4             TCGA-ZG-A9MC 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
            TCGA-ZG-A9N3             TCGA-ZG-A9ND             TCGA-ZG-A9NI 
"LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" "LOC100132247 WILD-TYPE" 
D41V9, continuous
D41V10, continuous
                        vv
clus                     ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LOC100132247 MUTATED       0                         0     0
  LOC100132247 WILD-TYPE     2                         7   147
D41V11, multiclass

Clustering(42) Variable = EMG1 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 484  10
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            494 
  EMG1 MUTATED EMG1 WILD-TYPE 
             0             10 
$`EMG1 MUTATED`
TCGA-HC-7078 TCGA-HC-7752 TCGA-VP-A872 TCGA-VP-A876 
       65.26        25.71       119.38       109.58 

$`EMG1 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 
       31.00         2.04         0.92        44.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        13.02        26.99         9.99 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        48.56        57.86        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-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        45.40        47.90        64.60        48.13        62.04 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        56.98        60.13        60.23        62.10        62.10 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       69.63        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-7115 
       62.76        58.45        60.23        41.85        60.10        88.34 
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-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       36.33        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-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG 
       18.41        21.90         7.56        11.61         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 
        9.27         9.83         8.75         4.54         4.31         4.77 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        28.83        22.36        17.23        25.94 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
       20.25        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        80.55        68.68        49.81        67.33 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        67.92        47.15        46.52        47.44        45.30 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81        64.01        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 
       58.22        56.75        64.18        50.73        52.93        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 
       27.91        30.97        35.44        28.18        32.68        26.01 
TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       29.79        23.93         6.08        30.94         3.68        19.76 
TCGA-HC-7077 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       69.53        38.93        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 
       40.14        28.60        40.08        32.91        30.87        38.17 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       36.26        35.84        31.69        23.57        30.84        17.46 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 
       23.70        24.59        23.80        17.16        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       17.85        24.56        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       27.85        30.38        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        15.55        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX 
        2.20         1.61        17.42         2.33         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE 
        4.41         4.93         9.53        25.48        18.84        19.30 
TCGA-HC-A9TH TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       27.75       109.25        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       40.04        33.01        25.32        30.94        30.81        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        17.85 
TCGA-J4-AATV TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       18.18        13.55        27.12        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CK TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        10.55        13.32        15.22        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        8.65         8.88        11.57       113.10        83.34        64.70 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        81.17       141.21        48.76        72.26       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        68.15       113.33        90.74        58.19 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        57.67        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       43.69        34.95        36.13        74.27       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID 
       65.82        31.79        32.91        63.48        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-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        62.96        16.21        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL 
       34.85        25.08        29.23        18.84         5.69         3.19 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT 
      140.19       122.17        86.14        18.12         0.89        17.29 
TCGA-TP-A8TV TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       20.05        47.64        28.18        58.88        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        61.68        64.04        30.38        15.58        22.55 
TCGA-V1-A8WW TCGA-V1-A8X3 TCGA-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA 
       35.44         6.64        63.52        82.16        94.36        20.91 
TCGA-V1-A9OF TCGA-V1-A9OH TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX 
       38.93        79.00        62.89        12.20        15.65        37.28 
TCGA-V1-A9OY TCGA-V1-A9Z7 TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI 
       35.08        28.73        27.19        17.75        49.87        53.92 
TCGA-V1-A9ZK TCGA-V1-A9ZR TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       45.47        44.75         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 
       25.18        15.81        41.42        44.91        25.78        16.31 
TCGA-VP-A875 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
       75.91       102.90        23.93        89.49        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  EMG1 MUTATED EMG1 WILD-TYPE 
         25.71           0.76 
  EMG1 MUTATED EMG1 WILD-TYPE 
        119.38         165.17 
  EMG1 MUTATED EMG1 WILD-TYPE 
         87.42          30.38 
[1] "25.7 - 119.4 (87.4)" "0.8 - 165.2 (30.4)" 
[1] "hr="     "2.9e+07"
D42V2, continuous
                vv
clus              T2  T3  T4
  EMG1 MUTATED     2   2   0
  EMG1 WILD-TYPE 186 291  10
D42V3, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T2            2            186
  T3            2            291
  T4            0             10
[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"
D42V4, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 342  79
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  342   79
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            342
  1            0             79
[1] 2 2
[1] FALSE
D42V5, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 391  59
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  391   59
     clus
vv    EMG1 MUTATED EMG1 WILD-TYPE
  NO             4            391
  YES            0             59
[1] 2 2
[1] FALSE
D42V6, binary
                cls
clus               0   1
  EMG1 MUTATED     3   1
  EMG1 WILD-TYPE 480  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      3    1
  EMG1 WILD-TYPE  480   14
                                        clus
vv                                       EMG1 MUTATED EMG1 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            480
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE            1             14
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EMG1 MUTATED     4   0   0   0
  EMG1 WILD-TYPE 312 147   5  15
D42V7, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  R0            4            312
  R1            0            147
  R2            0              5
  RX            0             15
[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"
D42V8, continuous
D42V9, continuous
D42V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     2
  EMG1 WILD-TYPE     2                         7   145
D42V11, multiclass
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            154 
    TCGA-CH-5753     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5772 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-EJ-5542     TCGA-EJ-7123 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-G9-6364     TCGA-HC-7233     TCGA-HC-7748 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7821     TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5740     TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5745     TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5754     TCGA-CH-5761 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5788 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5789     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-7115 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7789     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6353     TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6363     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7079     TCGA-HC-7080 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7738 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7818 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7820     TCGA-HI-7168     TCGA-HI-7169 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 

Clustering(43) Variable = CDH16 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  CDH16 MUTATED     4   0
  CDH16 WILD-TYPE 484  10
  CDH16 MUTATED CDH16 WILD-TYPE 
              4             494 
  CDH16 MUTATED CDH16 WILD-TYPE 
              0              10 
$`CDH16 MUTATED`
TCGA-2A-A8W3 TCGA-EJ-5521 TCGA-G9-A9S7 TCGA-J9-A52C 
       28.37        74.93        23.93         5.85 

$`CDH16 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F TCGA-CH-5737 
        3.68        44.84        41.82        20.22        11.51         2.99 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 
       24.03         2.04        13.02        26.99         9.99         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        48.56        57.86        19.56        13.32        56.55 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        38.50        45.73        46.92        30.31 
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-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        68.35        61.87        36.66        62.76        58.45 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 
       60.23        41.85        60.10        88.34        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-7792 
       25.68        38.70        36.03        28.24        36.33        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-A46E TCGA-EJ-A46F TCGA-EJ-A46H 
       24.85        25.18        20.58        17.23        25.74        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
        7.56        11.61         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 
        8.75         4.54         4.31         4.77        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       28.83        22.36        17.23        25.94        20.25        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       80.55        68.68        49.81        67.33        50.70        67.92 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 
       47.15        46.52        47.44        45.30        44.81        64.01 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       64.18        50.73        52.93        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-H9-7775 
       35.44        28.18        32.68        26.01        29.79         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
      109.25        88.24        82.92        43.69        20.19        40.04 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        30.81        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV 
       22.52        22.88        10.78        23.67        17.85        18.18 
TCGA-J4-AATZ TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       13.55        27.12        13.87         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIV 
       48.03         9.04         2.99        31.99        31.96        37.25 
TCGA-XK-AAIW TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU 
       40.04        30.58        41.39        36.95        47.15        51.81 
TCGA-XQ-A8TA TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ 
        4.80        25.32        32.61        17.29         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        75.75        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SI 
       16.83        56.52        41.46        45.14        28.77        53.06 
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-YL-A9WK TCGA-YL-A9WL 
        8.98        14.04        53.36        60.99        70.22        24.33 
TCGA-YL-A9WX TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       49.91        36.10         3.09        14.53        13.28        10.13 
TCGA-ZG-A9KY TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 
        4.27        11.67        42.81        37.94        36.43        29.85 
TCGA-ZG-A9L6 TCGA-ZG-A9L9 TCGA-ZG-A9LB TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS 
       22.59        20.28        19.17        12.43         3.78        16.96 
TCGA-ZG-A9LU TCGA-ZG-A9LY TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 
       19.04        12.16        22.75        17.98        14.96        11.47 
TCGA-ZG-A9ND TCGA-ZG-A9NI 
       13.48         4.34 

  CDH16 MUTATED CDH16 WILD-TYPE 
           5.85            0.76 
  CDH16 MUTATED CDH16 WILD-TYPE 
          74.93          165.17 
  CDH16 MUTATED CDH16 WILD-TYPE 
         26.150          30.545 
[1] "5.8 - 74.9 (26.1)"  "0.8 - 165.2 (30.5)"
[1] "hr="     "3300000"
D43V2, continuous
                 vv
clus               T2  T3  T4
  CDH16 MUTATED     0   4   0
  CDH16 WILD-TYPE 188 289  10
D43V3, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  T2             0             188
  T3             4             289
  T4             0              10
[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"
D43V4, binary
                 cls
clus                0   1
  CDH16 MUTATED     3   0
  CDH16 WILD-TYPE 343  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      3    0
  CDH16 WILD-TYPE  343   79
   clus
vv  CDH16 MUTATED CDH16 WILD-TYPE
  0             3             343
  1             0              79
[1] 2 2
[1] FALSE
D43V5, binary
                 cls
clus                0   1
  CDH16 MUTATED     3   1
  CDH16 WILD-TYPE 392  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      3    1
  CDH16 WILD-TYPE  392   58
     clus
vv    CDH16 MUTATED CDH16 WILD-TYPE
  NO              3             392
  YES             1              58
[1] 2 2
[1] FALSE
D43V6, binary
                 cls
clus                0   1
  CDH16 MUTATED     4   0
  CDH16 WILD-TYPE 479  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDH16 MUTATED      4    0
  CDH16 WILD-TYPE  479   15
                                        clus
vv                                       CDH16 MUTATED CDH16 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             479
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDH16 MUTATED     4   0   0   0
  CDH16 WILD-TYPE 312 147   5  15
D43V7, multiclass
    clus
vv   CDH16 MUTATED CDH16 WILD-TYPE
  R0             4             312
  R1             0             147
  R2             0               5
  RX             0              15
[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"
D43V8, continuous
D43V9, continuous
D43V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDH16 MUTATED       0                         0     1
  CDH16 WILD-TYPE     2                         7   146
D43V11, multiclass
[1] "Remove cluster labels:" "CDH16 MUTATED"         
clus
  CDH16 MUTATED CDH16 WILD-TYPE 
              1             155 
     TCGA-CH-5753      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5772 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-EJ-5542      TCGA-EJ-7123 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-G9-6364      TCGA-HC-7233      TCGA-HC-7748 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7821      TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5754      TCGA-CH-5761 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5788 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5522      TCGA-EJ-5524 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-7115      TCGA-EJ-7125 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7738 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7747      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HI-7168 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"CDH16 WILD-TYPE" "CDH16 WILD-TYPE" "CDH16 WILD-TYPE" 

Clustering(44) Variable = KRT25 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  KRT25 MUTATED     6   0
  KRT25 WILD-TYPE 482  10
  KRT25 MUTATED KRT25 WILD-TYPE 
              6             492 
  KRT25 MUTATED KRT25 WILD-TYPE 
              0              10 
$`KRT25 MUTATED`
TCGA-CH-5741 TCGA-CH-5768 TCGA-EJ-5525 TCGA-J4-8198 TCGA-XK-AAIV TCGA-ZG-A9LB 
       12.99        24.03        36.66        20.19        37.25        19.17 

$`KRT25 WILD-TYPE`
TCGA-CH-5753 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5772 TCGA-CH-5790 TCGA-CH-5791 
        1.02        12.00         1.02        15.98        32.02        33.01 
TCGA-EJ-5542 TCGA-EJ-7123 TCGA-EJ-7312 TCGA-EJ-7325 TCGA-EJ-7791 TCGA-EJ-A46B 
       49.74        84.56        36.13        35.18        36.76        21.60 
TCGA-EJ-A46G TCGA-EJ-A65J TCGA-EJ-A6RC TCGA-G9-6364 TCGA-HC-7233 TCGA-HC-7748 
       21.96        14.83        28.70        39.39        44.55        26.04 
TCGA-HC-7821 TCGA-HC-A6AQ TCGA-HC-A76W TCGA-J4-A83N TCGA-J9-A8CN TCGA-KC-A7FA 
       31.43         3.48         7.00        32.61        40.67        19.66 
TCGA-KK-A7AP TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8IB TCGA-QU-A6IM TCGA-XK-AAJ3 
        6.44        29.56        32.45         2.73        41.00        41.49 
TCGA-XK-AAK1 TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX 
       32.19        20.42        55.92        45.14        22.06        45.30 
TCGA-2A-A8W1 TCGA-2A-A8W3 TCGA-2A-AAYF TCGA-2A-AAYO TCGA-2A-AAYU TCGA-4L-AA1F 
        3.68        28.37        44.84        41.82        20.22        11.51 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06         1.02        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        2.04         0.92        44.02        23.01         1.02        15.06 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5792 TCGA-CH-5794 
        2.04        13.02        26.99         9.99         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-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       74.93        68.35        61.87        62.76        58.45        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7314 
       41.85        60.10        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-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-A46E TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I 
       25.18        20.58        17.23        25.74        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M 
       23.34        12.92        13.71        18.41        21.90         7.56 
TCGA-EJ-A6RA TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       11.61         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-EJ-AB20 TCGA-EJ-AB27 TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        4.54         4.31         4.77        28.41        15.42        28.83 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        25.94        20.25        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        80.55 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        67.33        50.70        67.92        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       46.52        47.44        45.30        44.81        64.01        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7509 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       50.73        52.93        38.96        27.91        30.97        35.44 
TCGA-G9-7523 TCGA-G9-7525 TCGA-G9-A9S0 TCGA-G9-A9S4 TCGA-G9-A9S7 TCGA-H9-7775 
       28.18        32.68        26.01        29.79        23.93         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7077 TCGA-HC-7078 TCGA-HC-7079 
       30.94         3.68        19.76        69.53        65.26        38.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54        40.14        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7736 TCGA-HC-7737 
       40.08        32.91        30.87        38.17        36.26        35.84 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57        30.84        17.46        23.70        24.59 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
       23.80        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       24.56        19.36        22.42        28.27        23.87        27.85 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
       30.38        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-A6AL 
       15.55        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         2.33         1.45         1.25         4.41 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HC-A9TE TCGA-HC-A9TH 
        4.93         9.53        25.48        18.84        19.30        27.75 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K 
      109.25        88.24        82.92        43.69        40.04        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        30.81        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-AATV TCGA-J4-AATZ 
       22.88        10.78        23.67        17.85        18.18        13.55 
TCGA-J4-AAU2 TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CK 
       27.12        13.87         5.85         6.97        10.62        10.55 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       13.32        15.22        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FD 
       44.35        43.66        21.86         2.99         8.65         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        83.34        64.70        86.40        81.17 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      141.21        48.76        72.26       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU 
       68.15       113.33        90.74        58.19        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        57.67        49.94        43.69        34.95 
TCGA-KK-A7B2 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       36.13        74.27       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        67.46        20.65        62.96 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
       16.21        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-MG-AAMC TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         5.69         3.19       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-TK-A8OK TCGA-TP-A8TT TCGA-TP-A8TV TCGA-V1-A8MF 
       86.14        18.12         0.89        17.29        20.05        47.64 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        58.88        16.70        14.73        39.29        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-V1-A9O5 TCGA-V1-A9O7 TCGA-V1-A9O9 TCGA-V1-A9OA TCGA-V1-A9OF TCGA-V1-A9OH 
       63.52        82.16        94.36        20.91        38.93        79.00 
TCGA-V1-A9OL TCGA-V1-A9OQ TCGA-V1-A9OT TCGA-V1-A9OX TCGA-V1-A9OY TCGA-V1-A9Z7 
       62.89        12.20        15.65        37.28        35.08        28.73 
TCGA-V1-A9Z8 TCGA-V1-A9Z9 TCGA-V1-A9ZG TCGA-V1-A9ZI TCGA-V1-A9ZK TCGA-V1-A9ZR 
       27.19        17.75        49.87        53.92        45.47        44.75 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        25.18        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VN-A943 TCGA-VP-A872 TCGA-VP-A875 
       41.42        44.91        25.78        16.31       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-VP-AA1N TCGA-WW-A8ZI 
       66.97        21.80        58.32        42.94        44.88        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19        12.36        37.05        48.03        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-XK-AAIR TCGA-XK-AAIW 
       48.03         9.04         2.99        31.99        31.96        40.04 
TCGA-XK-AAJA TCGA-XK-AAJP TCGA-XK-AAJR TCGA-XK-AAJT TCGA-XK-AAJU TCGA-XQ-A8TA 
       30.58        41.39        36.95        47.15        51.81         4.80 
TCGA-XQ-A8TB TCGA-Y6-A8TL TCGA-Y6-A9XI TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
       25.32        32.61        17.29         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-A8SI TCGA-YL-A8SJ 
       56.52        41.46        45.14        28.77        53.06        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-YL-A9WK TCGA-YL-A9WL TCGA-YL-A9WX 
       14.04        53.36        60.99        70.22        24.33        49.91 
TCGA-YL-A9WY TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ TCGA-ZG-A9KY 
       36.10         3.09        14.53        13.28        10.13         4.27 
TCGA-ZG-A9L0 TCGA-ZG-A9L1 TCGA-ZG-A9L2 TCGA-ZG-A9L4 TCGA-ZG-A9L5 TCGA-ZG-A9L6 
       11.67        42.81        37.94        36.43        29.85        22.59 
TCGA-ZG-A9L9 TCGA-ZG-A9LM TCGA-ZG-A9LN TCGA-ZG-A9LS TCGA-ZG-A9LU TCGA-ZG-A9LY 
       20.28        12.43         3.78        16.96        19.04        12.16 
TCGA-ZG-A9LZ TCGA-ZG-A9M4 TCGA-ZG-A9MC TCGA-ZG-A9N3 TCGA-ZG-A9ND TCGA-ZG-A9NI 
       22.75        17.98        14.96        11.47        13.48         4.34 

  KRT25 MUTATED KRT25 WILD-TYPE 
          12.99            0.76 
  KRT25 MUTATED KRT25 WILD-TYPE 
          37.25          165.17 
  KRT25 MUTATED KRT25 WILD-TYPE 
         22.110          30.545 
[1] "13.0 - 37.2 (22.1)" "0.8 - 165.2 (30.5)"
[1] "hr="     "3300000"
D44V2, continuous
                 vv
clus               T2  T3  T4
  KRT25 MUTATED     1   5   0
  KRT25 WILD-TYPE 187 288  10
D44V3, multiclass
    clus
vv   KRT25 MUTATED KRT25 WILD-TYPE
  T2             1             187
  T3             5             288
  T4             0              10
[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"
D44V4, binary
                 cls
clus                0   1
  KRT25 MUTATED     3   2
  KRT25 WILD-TYPE 343  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      3    2
  KRT25 WILD-TYPE  343   77
   clus
vv  KRT25 MUTATED KRT25 WILD-TYPE
  0             3             343
  1             2              77
[1] 2 2
[1] FALSE
D44V5, binary
                 cls
clus                0   1
  KRT25 MUTATED     4   2
  KRT25 WILD-TYPE 391  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      4    2
  KRT25 WILD-TYPE  391   57
     clus
vv    KRT25 MUTATED KRT25 WILD-TYPE
  NO              4             391
  YES             2              57
[1] 2 2
[1] FALSE
D44V6, binary
                 cls
clus                0   1
  KRT25 MUTATED     6   0
  KRT25 WILD-TYPE 477  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KRT25 MUTATED      6    0
  KRT25 WILD-TYPE  477   15
                                        clus
vv                                       KRT25 MUTATED KRT25 WILD-TYPE
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             477
  PROSTATE ADENOCARCINOMA, OTHER SUBTYPE             0              15
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KRT25 MUTATED     2   3   0   0
  KRT25 WILD-TYPE 314 144   5  15
D44V7, multiclass
    clus
vv   KRT25 MUTATED KRT25 WILD-TYPE
  R0             2             314
  R1             3             144
  R2             0               5
  RX             0              15
[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"
D44V8, continuous
D44V9, continuous
D44V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KRT25 MUTATED       0                         0     3
  KRT25 WILD-TYPE     2                         7   144
D44V11, multiclass
                           clus
vv                          KRT25 MUTATED KRT25 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[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"
