[1] "ofn"        "-oTKIRC-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/KIRC-TP/22506714/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/22815438/transformed.cor.cli.txt"

nPatients in clinical file=537, in cluster file=476, common to both=436
[1]  25 436
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             43             393 
  SETD2 MUTATED SETD2 WILD-TYPE 
             43             393 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            131             305 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            131             305 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             25             411 
  KDM5C MUTATED KDM5C WILD-TYPE 
             25             411 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          192           244 
  VHL MUTATED VHL WILD-TYPE 
          192           244 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            28            408 
  MTOR MUTATED MTOR WILD-TYPE 
            28            408 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             9            427 
  TP53 MUTATED TP53 WILD-TYPE 
             9            427 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            15            421 
  PTEN MUTATED PTEN WILD-TYPE 
            15            421 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             6            430 
  NEFH MUTATED NEFH WILD-TYPE 
             6            430 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            6           430 
  NF2 MUTATED NF2 WILD-TYPE 
            6           430 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           12           424 
  ATM MUTATED ATM WILD-TYPE 
           12           424 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               4              432 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               4              432 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              10              426 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              10              426 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             433 
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             433 
[1] "TFDP2 MUTATION ANALYSIS"
[1] 3
  TFDP2 MUTATED TFDP2 WILD-TYPE 
              4             432 
  TFDP2 MUTATED TFDP2 WILD-TYPE 
              4             432 
[1] "FAM200A MUTATION ANALYSIS"
[1] 3
  FAM200A MUTATED FAM200A WILD-TYPE 
                4               432 
  FAM200A MUTATED FAM200A WILD-TYPE 
                4               432 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             430 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             430 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             6            430 
  EGFR MUTATED EGFR WILD-TYPE 
             6            430 
[1] "SH3KBP1 MUTATION ANALYSIS"
[1] 3
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                3               433 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                3               433 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            432 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            432 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              10              426 
  ARID1A MUTATED ARID1A WILD-TYPE 
              10              426 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             433 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             433 
[1] "SLC16A9 MUTATION ANALYSIS"
[1] 3
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
                4               432 
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
                4               432 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             4            432 
  PCK1 MUTATED PCK1 WILD-TYPE 
             4            432 
[1] "CUL9 MUTATION ANALYSIS"
[1] 3
  CUL9 MUTATED CUL9 WILD-TYPE 
             7            429 
  CUL9 MUTATED CUL9 WILD-TYPE 
             7            429 
[1] "ZDHHC1 MUTATION ANALYSIS"
[1] 3
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
               4              432 
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
               4              432 
[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] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 436 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=145,	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=273,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "93"    "1"    
freq.contrast "1"     "93"   
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 436 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=57, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
213  54 162   7 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
213  54 162   7 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
213  54 162   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
213  54 162   7 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=4, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=4, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SETD2 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    24  19
  SETD2 WILD-TYPE 260 133
  SETD2 MUTATED SETD2 WILD-TYPE 
             43             393 
  SETD2 MUTATED SETD2 WILD-TYPE 
             19             133 
$`SETD2 MUTATED`
TCGA-A3-3358 TCGA-AK-3455 TCGA-B0-4712 TCGA-BP-5006 TCGA-BP-5178 TCGA-CJ-4891 
       42.97        22.45        43.96        27.62        62.86        26.93 
TCGA-A3-3311 TCGA-A3-3367 TCGA-AK-3431 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4811 
       39.16        74.63        73.68        57.70        58.45        46.59 
TCGA-B0-4814 TCGA-B0-4837 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5098 TCGA-B0-5121 
        5.52        45.30        36.85        11.90        52.08        48.82 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5699 TCGA-B2-4101 TCGA-B4-5835 TCGA-B8-4622 
       46.39        42.41       126.28        21.30         0.53        50.14 
TCGA-BP-4161 TCGA-BP-4329 TCGA-BP-4343 TCGA-BP-4774 TCGA-BP-4790 TCGA-BP-4983 
       90.28        27.78        62.86        61.97        36.53        46.45 
TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5682 
        6.35        19.82       131.08       133.71        18.87       122.83 
TCGA-CJ-5684 TCGA-CW-5580 TCGA-CW-5591 TCGA-CZ-4861 TCGA-CZ-5459 TCGA-CZ-5461 
       73.35        64.57        74.66        14.66        55.33        10.85 
TCGA-CZ-5470 
       12.69 

$`SETD2 WILD-TYPE`
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 
      109.91        58.49        28.73        19.73        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
       24.82        25.91         1.18       111.02        94.72        32.61 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       80.68        74.17        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5009 TCGA-BP-5168 
       27.22         5.82        45.07        41.62        35.90        48.10 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3313 TCGA-A3-3317 
       11.67        66.28        56.84        23.90        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       88.37        51.25        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
       65.10         5.98         2.14         6.64         3.25        15.72 
TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        0.59        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       65.29        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        34.36         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       51.02        38.43        56.98       129.67        85.78        86.47 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
       35.90         1.68        31.96        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        5.10         1.25         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       17.19        25.55        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       34.39        14.30        85.51       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       64.27        54.90        53.42        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
       10.82         5.33        56.91        68.38        15.78        48.95 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 
       37.02        37.48        35.21        28.87        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57        18.81        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
       25.71        22.32        25.25        18.15        62.10        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       53.42        62.66       119.64         7.36        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       85.78        66.31        78.18         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4866 
       25.45        47.08        69.21        58.75        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       90.54        91.69        94.45        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        31.10        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.53            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
         133.71          149.16 
  SETD2 MUTATED SETD2 WILD-TYPE 
          46.39           43.69 
[1] "0.5 - 133.7 (46.4)" "0.1 - 149.2 (43.7)"
[1] "hr=" "1.2"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        15        5        13       10
  SETD2 WILD-TYPE     193       38        99       62
D1V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              15             193
  STAGE II              5              38
  STAGE III            13              99
  STAGE IV             10              62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  SETD2 MUTATED    16   6  19   2
  SETD2 WILD-TYPE 197  48 143   5
D1V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            16             197
  T2             6              48
  T3            19             143
  T4             2               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                 cls
clus                0   1
  SETD2 MUTATED    22   0
  SETD2 WILD-TYPE 182  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     22    0
  SETD2 WILD-TYPE  182   15
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            22             182
  1             0              15
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    34   9
  SETD2 WILD-TYPE 332  61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     34    9
  SETD2 WILD-TYPE  332   61
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            34             332
  1             9              61
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    13  30
  SETD2 WILD-TYPE 142 251
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     13   30
  SETD2 WILD-TYPE  142  251
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            13             142
  MALE              30             251
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED       1                         2    38
  SETD2 WILD-TYPE     5                        18   367
D1V11, multiclass
                           clus
vv                          SETD2 MUTATED SETD2 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             2              18
  WHITE                                38             367
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  28
  SETD2 WILD-TYPE  20 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   28
  SETD2 WILD-TYPE   20  260
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              20
  NOT HISPANIC OR LATINO            28             260
[1] 2 2
[1] FALSE

Clustering(2) Variable = PBRM1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    86  45
  PBRM1 WILD-TYPE 198 107
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            131             305 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             45             107 
$`PBRM1 MUTATED`
TCGA-AK-3425 TCGA-B0-4815 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
      109.91        52.21       133.94        15.78        70.68       119.38 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
      111.02        32.61        27.22         5.82        45.07        41.62 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       48.10        49.15        27.02        75.58       103.43        46.16 
TCGA-DV-5566 TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       45.96        39.16        48.59        36.36        37.38        48.82 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3387 TCGA-AK-3431 TCGA-AK-3434 
       51.25        74.63        53.29        20.28        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4816 
      109.51        38.40        82.45         2.14        58.45        45.07 
TCGA-B0-4818 TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       16.77        10.09        56.68        26.07         2.27        36.85 
TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5110 
       25.32        10.95         2.24        90.48        30.48        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5696 
       38.63        52.73        41.88        38.43        46.39        85.78 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      126.28        73.84       149.16        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-4099 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 
       91.46        31.96        12.00         5.10         4.64         0.23 
TCGA-B8-4148 TCGA-B8-4154 TCGA-B8-5158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4176 
       49.97        45.37        40.04        85.51        90.28        64.27 
TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4774 TCGA-BP-4801 TCGA-BP-4960 
       27.78         0.07        52.24        61.97        36.95        71.41 
TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       61.22        45.50        47.11        36.07        33.34        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5183 
       36.95         3.88         6.35        79.30        74.40        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 
       37.25        22.78        13.35        19.82        34.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4887 TCGA-CJ-4888 
       46.55        11.05        79.66       116.84        30.64        51.52 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 
       51.29        49.18        50.33        54.48        38.56         4.57 
TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 
       18.81       133.71        18.87        22.32       122.83        73.35 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5589 TCGA-CZ-4853 TCGA-CZ-5453 TCGA-CZ-5454 
        7.36        64.57        78.18        25.45        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 
       18.44        79.63        94.45        10.85        84.30        22.52 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5907 
       12.69        80.19        12.26        62.63         4.18 

$`PBRM1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
       42.97        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       18.51       112.80       126.05        24.82        25.91         1.18 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       94.72        80.68        74.17        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5199 
       25.81        27.62        35.90        62.86        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 
       31.27        63.25        26.93        27.65       108.56       118.85 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5569 
        0.59       107.54         5.46        43.69        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3347 
       66.28        56.84        23.90        24.16        49.02        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       45.53        88.37        74.76        43.20        55.76        65.52 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3440 TCGA-AK-3443 
      117.80       122.56       109.41        15.78        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 
       78.64        94.29        83.21        37.58        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
       65.10         5.98        57.70         6.64         3.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 
       46.59         0.59         5.52        33.50         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       14.93        54.48        29.10        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       27.42        53.88         6.71        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       39.45        29.03        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 
       11.90        34.36         7.30        15.09         8.05        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 
       52.08        15.95        62.89        90.87        52.54        58.59 
TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 
       19.30        52.87        51.02        48.82        56.98        42.41 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 
      129.67        86.47        80.91        71.41       105.37       123.09 
TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-5633 
      130.65        32.61        35.90         1.68        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 
       21.57         1.25         0.53         5.46         0.36        23.31 
TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       16.80        42.71        25.05        17.19        25.55        50.14 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4162 
        6.38        48.53         0.53        34.39        14.30       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4338 
       62.24        61.78        54.90        53.42        62.07        93.99 
TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
       10.82         5.33        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 
       36.53        36.39        10.98         6.71        47.97        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       58.68        60.30         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4991 TCGA-BP-4992 
       49.38         6.94        14.93        46.45        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       35.21        28.87         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
        9.63        38.30        37.22        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       24.62        33.47         0.95        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      114.41        54.61        58.95        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
       61.91        57.83       113.46        64.18        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 
       47.67        49.97        49.28        45.14         3.06       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       72.00       129.40        25.71        25.25        18.15        62.10 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       67.00        53.42        62.66       119.64        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       85.78        66.31        74.66         1.35        83.90        18.77 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       63.42        58.82        90.54        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 
       21.76         2.40         1.94        31.10        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        18.12         3.91         6.77 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.36 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         149.16          131.08 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          45.96           43.20 
[1] "0.1 - 149.2 (46.0)" "0.4 - 131.1 (43.2)"
[1] "hr=" "1.1"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        65       12        32       22
  PBRM1 WILD-TYPE     143       31        80       50
D2V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              65             143
  STAGE II             12              31
  STAGE III            32              80
  STAGE IV             22              50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PBRM1 MUTATED    66  19  46   0
  PBRM1 WILD-TYPE 147  35 116   7
D2V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            66             147
  T2            19              35
  T3            46             116
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                 cls
clus                0   1
  PBRM1 MUTATED    59   2
  PBRM1 WILD-TYPE 145  13
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     59    2
  PBRM1 WILD-TYPE  145   13
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0            59             145
  1             2              13
[1] 2 2
[1] FALSE
D2V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   109  22
  PBRM1 WILD-TYPE 257  48
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    109   22
  PBRM1 WILD-TYPE  257   48
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0           109             257
  1            22              48
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    44  87
  PBRM1 WILD-TYPE 111 194
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     44   87
  PBRM1 WILD-TYPE  111  194
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            44             111
  MALE              87             194
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1               6 
     TCGA-B8-4621      TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-4146 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
D2V10, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1               3 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5550 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       1                         3   123
  PBRM1 WILD-TYPE     5                        17   282
D2V11, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 1               5
  BLACK OR AFRICAN AMERICAN             3              17
  WHITE                               123             282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                 cls
clus                0   1
  PBRM1 MUTATED     5  84
  PBRM1 WILD-TYPE  16 204
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      5   84
  PBRM1 WILD-TYPE   16  204
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 5              16
  NOT HISPANIC OR LATINO            84             204
[1] 2 2
[1] FALSE

Clustering(3) Variable = KDM5C MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    13  12
  KDM5C WILD-TYPE 271 140
  KDM5C MUTATED KDM5C WILD-TYPE 
             25             411 
  KDM5C MUTATED KDM5C WILD-TYPE 
             12             140 
$`KDM5C MUTATED`
TCGA-B0-5698 TCGA-BP-5189 TCGA-A3-3331 TCGA-AK-3430 TCGA-AK-3458 TCGA-B0-4694 
      119.38        27.02        48.82        15.78        38.40         3.48 
TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4828 TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-5077 
       58.45        45.07        10.09        45.30        10.29        43.30 
TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5108 TCGA-B2-5641 TCGA-BP-4159 TCGA-BP-4351 
       10.95        52.54        58.59        21.57        85.51        31.89 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5190 TCGA-BP-5202 TCGA-CJ-4871 TCGA-CW-5581 
       18.51         6.35        33.24         0.95        79.66        92.02 
TCGA-CZ-5467 
        2.40 

$`KDM5C WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
       70.68       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 
       27.62        35.90        48.10        62.86        49.15        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       44.55        31.27        63.25        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       56.84        23.90        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 
       36.36        37.38        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
       20.28       117.80       122.56       109.41        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       37.58        82.45        72.89        12.13        40.70         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        4.57         2.53        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       57.70         6.64         3.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
        5.52        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       54.48        29.10        78.44        40.70        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 
       29.03         2.27        36.85        70.52        20.94        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5095 
       11.90        34.36         7.30        25.32        15.09         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       90.48        30.48        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B4-5377 
       35.90         1.68        31.96        21.30        31.66        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4161 TCGA-BP-4162 
       48.53         0.53        34.39        14.30        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 
       49.84        49.08        44.94        12.23        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        43.00        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 
       37.25        37.22        22.78        13.35        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        33.47        19.82        34.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       64.57        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
         119.38          149.16 
  KDM5C MUTATED KDM5C WILD-TYPE 
          33.24           45.07 
[1] "0.9 - 119.4 (33.2)" "0.1 - 149.2 (45.1)"
[1] "hr=" "1.7"
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        13        1         7        4
  KDM5C WILD-TYPE     195       42       105       68
D3V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              13             195
  STAGE II              1              42
  STAGE III             7             105
  STAGE IV              4              68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM5C MUTATED    13   2  10   0
  KDM5C WILD-TYPE 200  52 152   7
D3V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            13             200
  T2             2              52
  T3            10             152
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                 cls
clus                0   1
  KDM5C MUTATED    13   1
  KDM5C WILD-TYPE 191  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     13    1
  KDM5C WILD-TYPE  191   14
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            13             191
  1             1              14
[1] 2 2
[1] FALSE
D3V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    21   4
  KDM5C WILD-TYPE 345  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     21    4
  KDM5C WILD-TYPE  345   66
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            21             345
  1             4              66
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     3  22
  KDM5C WILD-TYPE 152 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      3   22
  KDM5C WILD-TYPE  152  259
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             3             152
  MALE              22             259
[1] 2 2
[1] FALSE
D3V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              36 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-AK-3428      TCGA-B0-4838 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
D3V9, continuous
D3V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED       0                         1    24
  KDM5C WILD-TYPE     6                        19   381
D3V11, multiclass
                           clus
vv                          KDM5C MUTATED KDM5C WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1              19
  WHITE                                24             381
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                 cls
clus                0   1
  KDM5C MUTATED     0  20
  KDM5C WILD-TYPE  21 268
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   20
  KDM5C WILD-TYPE   21  268
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO            20             268
[1] 2 2
[1] FALSE

Clustering(4) Variable = VHL MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  VHL MUTATED   123  69
  VHL WILD-TYPE 161  83
  VHL MUTATED VHL WILD-TYPE 
          192           244 
  VHL MUTATED VHL WILD-TYPE 
           69            83 
$`VHL MUTATED`
TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       58.49        22.45        43.96        18.51       112.80       133.94 
TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4164 TCGA-BP-4342 
       70.68       126.05        24.82         1.18        32.61        74.17 
TCGA-BP-4762 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       44.15         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5181 TCGA-BP-5199 
       45.07        41.62        27.62        35.90        49.15        44.55 
TCGA-CJ-4636 TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
       63.25        27.65       118.85        75.58       103.43         0.59 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3385 
       48.82        45.53        51.25        53.29        55.76        65.52 
TCGA-AK-3445 TCGA-AK-3458 TCGA-B0-4690 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
       78.64        38.40         1.41        65.10         5.98         2.14 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4819 
        6.64         3.25        15.72         5.52        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 
       56.68        65.29        26.07        36.85        70.52        43.30 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       11.90        25.32         8.05         2.24        21.86        15.95 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 
       90.87        52.54        30.48        58.59        38.63        52.73 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5709 
       42.41       129.67        85.78        73.84       149.16       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3924 TCGA-B4-5832 TCGA-B4-5836 
       79.89       131.15        91.46        35.90         5.10         4.64 
TCGA-B4-5843 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 
        0.36        49.97        42.71        25.05        45.37        23.74 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4159 TCGA-BP-4166 
       27.02        24.23         6.38         0.53        85.51         0.43 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4349 TCGA-BP-4355 
       89.36        27.78        18.48        52.24        12.23        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4771 TCGA-BP-4789 
       72.59        77.98        41.75        71.80         5.33        48.95 
TCGA-BP-4798 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       10.98        71.41        63.62        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 
       57.40        14.24         6.94        47.11        14.93        33.34 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
        3.88        46.45        16.47        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 
       30.64        52.27         9.63        74.40        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       22.78        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4872 
       19.82       115.00        73.22        14.17        11.05        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4892 TCGA-CJ-4900 TCGA-CJ-4903 
      116.84        57.83       113.46        50.01        56.35        51.29 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5676 
       50.33        54.48        45.14         3.06         4.57       133.71 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
       25.71        25.25        73.35        67.00        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 
        7.36        64.57        81.83        66.31        74.66        83.90 
TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5465 
       25.45        69.21        14.66        91.69        94.45        84.30 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       14.63        62.63        18.12         3.91         6.77         4.18 

$`VHL WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5694 
       42.97       109.91        28.73        19.73        52.21        15.78 
TCGA-B0-5698 TCGA-B8-4621 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4760 
      119.38        25.91       111.02        94.72        80.68        77.62 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4993 TCGA-BP-5168 
       60.59        11.64        20.38        37.25         5.82        48.10 
TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4891 TCGA-CJ-4904 
       62.86        27.02        31.79        31.27        26.93       108.56 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       46.16       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3357 
       49.02        48.59        36.36        37.38        52.93        88.37 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       74.63        74.76        43.20        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       46.78        94.29        83.21        37.58        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       12.13        40.70         4.57         2.53         3.48        19.00 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 
       57.70        58.45        46.59         0.59        45.07        33.50 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 
       40.70        45.30        27.42        53.88         6.71        10.52 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5080 
       10.29        39.45        29.03         2.27        20.94        11.24 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5100 
       34.36         7.30        15.09        10.95        52.08        62.89 
TCGA-B0-5104 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       90.48        19.30        66.05        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5697 TCGA-B0-5699 
       38.43        48.82        46.39        56.98        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5712 TCGA-B2-3923 
       80.91        71.41       105.37       123.09        89.49        32.61 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         5.46         0.23        23.31        16.80 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5545 
       17.19        25.55        50.14        40.04         0.85        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4161 TCGA-BP-4162 
       16.60        48.53        34.39        14.30        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       93.34        99.85        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       64.27        54.90        53.42        62.07         0.07        93.99 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.84        49.08        44.94        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       33.99        12.30         5.98        48.07        13.15        10.82 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 
       61.97        56.91        68.38        15.78        36.53        36.39 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-4972 
       36.95         6.71        47.97        58.68        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4994 
       45.50        36.07        46.45        31.30        36.95        43.00 
TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5200 
       18.51        28.87        38.30        37.22        13.35        34.95 
TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
        0.95        46.55       106.16       114.41        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        79.66        74.27        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 
       64.27        71.87        66.21        61.91        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       51.52        63.98       115.69        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4913 
       50.24        47.67        49.97        49.18        49.28        38.56 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       18.81       131.08        72.00       129.40        18.87        22.32 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5585 
       18.15       122.83        62.10        53.42        92.02        85.78 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4863 
       78.18         1.35        18.77        47.08        58.75        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        90.54        55.33        10.85        10.22        21.76 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5988 
       22.52         2.40         1.94        22.78 

  VHL MUTATED VHL WILD-TYPE 
         0.36          0.07 
  VHL MUTATED VHL WILD-TYPE 
       149.16        131.08 
  VHL MUTATED VHL WILD-TYPE 
       42.080        46.275 
[1] "0.4 - 149.2 (42.1)" "0.1 - 131.1 (46.3)"
[1] "hr=" "1.1"
D4V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED       102       16        44       29
  VHL WILD-TYPE     106       27        68       43
D4V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I           102           106
  STAGE II           16            27
  STAGE III          44            68
  STAGE IV           29            43
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  VHL MUTATED   103  20  64   5
  VHL WILD-TYPE 110  34  98   2
D4V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1         103           110
  T2          20            34
  T3          64            98
  T4           5             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
               cls
clus              0   1
  VHL MUTATED    85   5
  VHL WILD-TYPE 119  10
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     85    5
  VHL WILD-TYPE  119   10
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0          85           119
  1           5            10
[1] 2 2
[1] FALSE
D4V6, binary
               cls
clus              0   1
  VHL MUTATED   163  29
  VHL WILD-TYPE 203  41
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    163   29
  VHL WILD-TYPE  203   41
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0         163           203
  1          29            41
[1] 2 2
[1] FALSE
D4V7, binary
               cls
clus              0   1
  VHL MUTATED    73 119
  VHL WILD-TYPE  82 162
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     73  119
  VHL WILD-TYPE   82  162
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          73            82
  MALE           119           162
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
[1] "Remove cluster labels:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            1             6 
   TCGA-B8-4621    TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-5158    TCGA-B8-5164 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B8-5550 
"VHL WILD-TYPE" 
D4V10, continuous
[1] "Remove cluster labels:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            1             3 
   TCGA-AK-3451    TCGA-B8-5158    TCGA-B8-5550 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED       2                         2   186
  VHL WILD-TYPE     4                        18   219
D4V11, multiclass
                           clus
vv                          VHL MUTATED VHL WILD-TYPE
  ASIAN                               2             4
  BLACK OR AFRICAN AMERICAN           2            18
  WHITE                             186           219
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
               cls
clus              0   1
  VHL MUTATED     8 121
  VHL WILD-TYPE  13 167
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      8  121
  VHL WILD-TYPE   13  167
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               8            13
  NOT HISPANIC OR LATINO         121           167
[1] 2 2
[1] FALSE

Clustering(5) Variable = MTOR MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    13  15
  MTOR WILD-TYPE 271 137
  MTOR MUTATED MTOR WILD-TYPE 
            28            408 
  MTOR MUTATED MTOR WILD-TYPE 
            15            137 
$`MTOR MUTATED`
TCGA-B0-5691 TCGA-CJ-6027 TCGA-A3-3347 TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 
      112.80       118.85        52.93       109.41        15.72        29.10 
TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5696 
       39.45        36.85        52.08        62.89        51.02        85.78 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5712 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 
       86.47        80.91        89.49         5.10         4.64         0.23 
TCGA-BP-5175 TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4887 TCGA-CJ-4907 TCGA-CJ-5679 
       30.64        52.27        11.05        30.64        49.28        22.32 
TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5987 
       64.57        47.08       107.41        14.63 

$`MTOR WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       43.96        52.21        18.51       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       56.84        23.90        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 
       36.36        37.38        48.82        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       20.28       117.80       122.56        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
        6.02        36.53        14.93        54.48        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.52        10.29        65.29        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       21.86        15.95        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       52.87        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      129.67       126.28        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3923 
      123.09       130.65        79.89       131.15        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 
       12.00         1.25         0.53         5.46         0.36        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
        2.04        74.20         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 
       66.21        61.91        57.83       113.46        64.18        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 
       67.00        53.42        62.66       119.64         7.36        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       83.90        18.77        25.45        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       63.39        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  MTOR MUTATED MTOR WILD-TYPE 
          0.23           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        118.85         149.16 
  MTOR MUTATED MTOR WILD-TYPE 
        50.150         43.825 
[1] "0.2 - 118.8 (50.2)" "0.1 - 149.2 (43.8)"
[1] "hr=" "1.4"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED         9        3         9        7
  MTOR WILD-TYPE     199       40       103       65
D5V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I              9            199
  STAGE II             3             40
  STAGE III            9            103
  STAGE IV             7             65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTOR MUTATED    10   4  14   0
  MTOR WILD-TYPE 203  50 148   7
D5V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1           10            203
  T2            4             50
  T3           14            148
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                cls
clus               0   1
  MTOR MUTATED    15   2
  MTOR WILD-TYPE 189  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     15    2
  MTOR WILD-TYPE  189   13
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           15            189
  1            2             13
[1] 2 2
[1] FALSE
D5V6, binary
                cls
clus               0   1
  MTOR MUTATED    21   7
  MTOR WILD-TYPE 345  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     21    7
  MTOR WILD-TYPE  345   63
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           21            345
  1            7             63
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  MTOR MUTATED    14  14
  MTOR WILD-TYPE 141 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     14   14
  MTOR WILD-TYPE  141  267
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           14            141
  MALE             14            267
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED       0                         3    25
  MTOR WILD-TYPE     6                        17   380
D5V11, multiclass
                           clus
vv                          MTOR MUTATED MTOR WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            3             17
  WHITE                               25            380
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                cls
clus               0   1
  MTOR MUTATED     1  25
  MTOR WILD-TYPE  20 263
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   25
  MTOR WILD-TYPE   20  263
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             20
  NOT HISPANIC OR LATINO           25            263
[1] 2 2
[1] FALSE

Clustering(6) Variable = TP53 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     5   4
  TP53 WILD-TYPE 279 148
  TP53 MUTATED TP53 WILD-TYPE 
             9            427 
  TP53 MUTATED TP53 WILD-TYPE 
             4            148 
$`TP53 MUTATED`
TCGA-CZ-4865 TCGA-AK-3440 TCGA-B0-4710 TCGA-B0-5098 TCGA-B0-5117 TCGA-BP-4176 
        5.46        94.19        57.70        52.08        52.87        64.27 
TCGA-BP-4770 TCGA-CJ-5677 TCGA-CZ-5463 
       10.82        25.71        21.76 

$`TP53 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
        0.59       107.54        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 
       15.78        73.68        68.61       109.51        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       19.00        65.10         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       71.80        48.07        13.15         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       129.40       133.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  TP53 MUTATED TP53 WILD-TYPE 
          5.46           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
         94.19         149.16 
  TP53 MUTATED TP53 WILD-TYPE 
         52.08          44.15 
[1] "5.5 - 94.2 (52.1)"  "0.1 - 149.2 (44.1)"
[1] "hr=" "1.4"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         5        1         1        2
  TP53 WILD-TYPE     203       42       111       70
D6V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              5            203
  STAGE II             1             42
  STAGE III            1            111
  STAGE IV             2             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TP53 MUTATED     5   1   2   1
  TP53 WILD-TYPE 208  53 160   6
D6V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            5            208
  T2            1             53
  T3            2            160
  T4            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                cls
clus               0   1
  TP53 MUTATED     2   0
  TP53 WILD-TYPE 202  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2    0
  TP53 WILD-TYPE  202   15
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            2            202
  1            0             15
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus               0   1
  TP53 MUTATED     8   1
  TP53 WILD-TYPE 358  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      8    1
  TP53 WILD-TYPE  358   69
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            8            358
  1            1             69
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  TP53 MUTATED     5   4
  TP53 WILD-TYPE 150 277
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5    4
  TP53 WILD-TYPE  150  277
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            5            150
  MALE              4            277
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         1     8
  TP53 WILD-TYPE     6                        19   397
D6V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1             19
  WHITE                                8            397
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                cls
clus               0   1
  TP53 MUTATED     0   6
  TP53 WILD-TYPE  21 282
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    6
  TP53 WILD-TYPE   21  282
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            6            282
[1] 2 2
[1] FALSE

Clustering(7) Variable = PTEN MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    10   5
  PTEN WILD-TYPE 274 147
  PTEN MUTATED PTEN WILD-TYPE 
            15            421 
  PTEN MUTATED PTEN WILD-TYPE 
             5            147 
$`PTEN MUTATED`
TCGA-B8-4621 TCGA-BP-5199 TCGA-DV-5568 TCGA-AK-3427 TCGA-B0-4694 TCGA-B0-4810 
       25.91        44.55        12.16       117.80         3.48        15.72 
TCGA-B0-4843 TCGA-B8-5158 TCGA-BP-4161 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4351 
       10.52        40.04        90.28        53.42        49.84        31.89 
TCGA-BP-5010 TCGA-CJ-4871 TCGA-EU-5907 
       28.87        79.66         4.18 

$`PTEN WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4158 
       70.68       119.38       126.05        24.82         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.79        31.27        63.25        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
        5.46        43.69        45.96        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       23.90        39.16        24.16        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       20.28       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        1.41         4.57         2.53        19.00        65.10         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       85.51       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.02        37.48        35.21         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 
        6.77 

  PTEN MUTATED PTEN WILD-TYPE 
          3.48           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
        117.80         149.16 
  PTEN MUTATED PTEN WILD-TYPE 
         31.89          45.07 
[1] "3.5 - 117.8 (31.9)" "0.1 - 149.2 (45.1)"
[1] "hr=" "1.1"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         5        1         8        1
  PTEN WILD-TYPE     203       42       104       71
D7V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              5            203
  STAGE II             1             42
  STAGE III            8            104
  STAGE IV             1             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED     5   1   9   0
  PTEN WILD-TYPE 208  53 153   7
D7V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            5            208
  T2            1             53
  T3            9            153
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                cls
clus               0   1
  PTEN MUTATED     8   2
  PTEN WILD-TYPE 196  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8    2
  PTEN WILD-TYPE  196   13
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            8            196
  1            2             13
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus               0   1
  PTEN MUTATED    14   1
  PTEN WILD-TYPE 352  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     14    1
  PTEN WILD-TYPE  352   69
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           14            352
  1            1             69
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  PTEN MUTATED     2  13
  PTEN WILD-TYPE 153 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   13
  PTEN WILD-TYPE  153  268
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            2            153
  MALE             13            268
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2              5 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-5164 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-B8-5550 
"PTEN WILD-TYPE" 
D7V10, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             1              3 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5550 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         1    14
  PTEN WILD-TYPE     6                        19   391
D7V11, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            1             19
  WHITE                               14            391
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                cls
clus               0   1
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  21 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   21  276
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO           12            276
[1] 2 2
[1] FALSE

Clustering(8) Variable = NEFH MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     4   2
  NEFH WILD-TYPE 280 150
  NEFH MUTATED NEFH WILD-TYPE 
             6            430 
  NEFH MUTATED NEFH WILD-TYPE 
             2            150 
$`NEFH MUTATED`
TCGA-AK-3451 TCGA-B0-4706 TCGA-B8-4622 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CZ-5456 
       94.29         2.14        50.14        18.15        62.10        79.63 

$`NEFH WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       46.78        78.64        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4713 
        3.48        19.00        65.10         5.98        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 
       42.71        25.05        45.37        17.19        25.55        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      133.71        25.71        18.87        22.32        25.25       122.83 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  NEFH MUTATED NEFH WILD-TYPE 
          2.14           0.07 
  NEFH MUTATED NEFH WILD-TYPE 
         94.29         149.16 
  NEFH MUTATED NEFH WILD-TYPE 
        56.120         44.055 
[1] "2.1 - 94.3 (56.1)"  "0.1 - 149.2 (44.1)"
[1] "hr=" "1.2"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         1        2         1        2
  NEFH WILD-TYPE     207       41       111       70
D8V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              1            207
  STAGE II             2             41
  STAGE III            1            111
  STAGE IV             2             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  NEFH MUTATED     1   2   3   0
  NEFH WILD-TYPE 212  52 159   7
D8V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            1            212
  T2            2             52
  T3            3            159
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                cls
clus               0   1
  NEFH MUTATED     3   0
  NEFH WILD-TYPE 201  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      3    0
  NEFH WILD-TYPE  201   15
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            3            201
  1            0             15
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus               0   1
  NEFH MUTATED     4   2
  NEFH WILD-TYPE 362  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    2
  NEFH WILD-TYPE  362   68
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            4            362
  1            2             68
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  NEFH MUTATED     1   5
  NEFH WILD-TYPE 154 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      1    5
  NEFH WILD-TYPE  154  276
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            1            154
  MALE              5            276
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             35 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-AK-3428     TCGA-AK-3430 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-5158     TCGA-CJ-6028 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-5457     TCGA-CZ-5458 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-EU-5904 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5906     TCGA-EU-5907 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D8V9, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1              6 
    TCGA-B8-4621     TCGA-AK-3445     TCGA-B8-4146     TCGA-B8-5158 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5550 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D8V10, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1              3 
    TCGA-AK-3445     TCGA-B8-5158     TCGA-B8-5550 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED       0                         0     6
  NEFH WILD-TYPE     6                        20   399
D8V11, multiclass
                           clus
vv                          NEFH MUTATED NEFH WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0             20
  WHITE                                6            399
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                cls
clus               0   1
  NEFH MUTATED     0   5
  NEFH WILD-TYPE  21 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    5
  NEFH WILD-TYPE   21  283
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            5            283
[1] 2 2
[1] FALSE

Clustering(9) Variable = NF2 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     3   3
  NF2 WILD-TYPE 281 149
  NF2 MUTATED NF2 WILD-TYPE 
            6           430 
  NF2 MUTATED NF2 WILD-TYPE 
            3           149 
$`NF2 MUTATED`
TCGA-BP-4986 TCGA-B0-5084 TCGA-B0-5098 TCGA-B8-4153 TCGA-CJ-4638 TCGA-CJ-4901 
       25.81         7.30        52.08        25.05        14.17        47.67 

$`NF2 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       61.51        53.65        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       34.36        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       56.35        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  NF2 MUTATED NF2 WILD-TYPE 
         7.30          0.07 
  NF2 MUTATED NF2 WILD-TYPE 
        52.08        149.16 
  NF2 MUTATED NF2 WILD-TYPE 
       25.430        44.745 
[1] "7.3 - 52.1 (25.4)"  "0.1 - 149.2 (44.7)"
[1] "hr=" "2.4"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         2        2
  NF2 WILD-TYPE     206       43       110       70
D9V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2           206
  STAGE II            0            43
  STAGE III           2           110
  STAGE IV            2            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF2 MUTATED     2   0   4   0
  NF2 WILD-TYPE 211  54 158   7
D9V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           2           211
  T2           0            54
  T3           4           158
  T4           0             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
               cls
clus              0   1
  NF2 MUTATED     1   2
  NF2 WILD-TYPE 203  13
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    2
  NF2 WILD-TYPE  203   13
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           1           203
  1           2            13
[1] 2 2
[1] FALSE
D9V6, binary
               cls
clus              0   1
  NF2 MUTATED     4   2
  NF2 WILD-TYPE 362  68
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      4    2
  NF2 WILD-TYPE  362   68
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           4           362
  1           2            68
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  NF2 MUTATED     2   4
  NF2 WILD-TYPE 153 277
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    4
  NF2 WILD-TYPE  153  277
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           2           153
  MALE             4           277
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED       0                         1     5
  NF2 WILD-TYPE     6                        19   400
D9V11, multiclass
                           clus
vv                          NF2 MUTATED NF2 WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           1            19
  WHITE                               5           400
[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"
D9V12, binary
               cls
clus              0   1
  NF2 MUTATED     1   5
  NF2 WILD-TYPE  20 283
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    5
  NF2 WILD-TYPE   20  283
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1            20
  NOT HISPANIC OR LATINO           5           283
[1] 2 2
[1] FALSE

Clustering(10) Variable = ATM MUTATION ANALYSIS
D10V1, survival
               sevent
clus2             0   1
  ATM MUTATED     9   3
  ATM WILD-TYPE 275 149
  ATM MUTATED ATM WILD-TYPE 
           12           424 
  ATM MUTATED ATM WILD-TYPE 
            3           149 
$`ATM MUTATED`
TCGA-CJ-4904 TCGA-B0-5097 TCGA-B0-5703 TCGA-B8-4622 TCGA-BP-4964 TCGA-BP-5173 
      108.56        21.86        73.84        50.14        61.22         2.04 
TCGA-CJ-4639 TCGA-CJ-4900 TCGA-CJ-5686 TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 
      106.16        56.35        67.00        14.66        63.42        12.26 

$`ATM WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       27.65       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
      126.28        80.91        71.41       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
       25.05        45.37        17.19        25.55        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 
       71.41        63.62        58.68        60.30         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
       79.30        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45       109.84        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15       122.83        62.10        73.35        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4866 
       25.45        47.08        69.21        58.75        63.39       107.41 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        67.96        65.65        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  ATM MUTATED ATM WILD-TYPE 
         2.04          0.07 
  ATM MUTATED ATM WILD-TYPE 
       108.56        149.16 
  ATM MUTATED ATM WILD-TYPE 
       58.785        43.825 
[1] "2.0 - 108.6 (58.8)" "0.1 - 149.2 (43.8)"
[1] "hr=" "1.6"
D10V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         5        3         1        3
  ATM WILD-TYPE     203       40       111       69
D10V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             5           203
  STAGE II            3            40
  STAGE III           1           111
  STAGE IV            3            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED     5   3   3   1
  ATM WILD-TYPE 208  51 159   6
D10V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           5           208
  T2           3            51
  T3           3           159
  T4           1             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
               cls
clus              0   1
  ATM MUTATED     8   1
  ATM WILD-TYPE 196  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      8    1
  ATM WILD-TYPE  196   14
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           8           196
  1           1            14
[1] 2 2
[1] FALSE
D10V6, binary
               cls
clus              0   1
  ATM MUTATED     9   3
  ATM WILD-TYPE 357  67
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      9    3
  ATM WILD-TYPE  357   67
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           9           357
  1           3            67
[1] 2 2
[1] FALSE
D10V7, binary
               cls
clus              0   1
  ATM MUTATED     6   6
  ATM WILD-TYPE 149 275
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      6    6
  ATM WILD-TYPE  149  275
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           6           149
  MALE             6           275
[1] 2 2
[1] FALSE
D10V8, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            2            35 
   TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4862    TCGA-DV-5565    TCGA-DV-5566 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-AK-3428    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-5158    TCGA-CJ-6028    TCGA-CZ-4858 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458    TCGA-CZ-5465    TCGA-CZ-5469 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5982    TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5906    TCGA-EU-5907 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
D10V9, continuous
D10V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         0    12
  ATM WILD-TYPE     6                        20   393
D10V11, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             6
  BLACK OR AFRICAN AMERICAN           0            20
  WHITE                              12           393
[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"
D10V12, binary
               cls
clus              0   1
  ATM MUTATED     1   6
  ATM WILD-TYPE  20 282
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    6
  ATM WILD-TYPE   20  282
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            20
  NOT HISPANIC OR LATINO           6           282
[1] 2 2
[1] FALSE

Clustering(11) Variable = NUDT11 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     4   0
  NUDT11 WILD-TYPE 280 152
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               4              432 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               0              152 
$`NUDT11 MUTATED`
TCGA-B4-5838 TCGA-B8-4153 TCGA-BP-5195 TCGA-BP-5202 
        5.46        25.05        24.62         0.95 

$`NUDT11 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       49.97        42.71        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 
       13.41        33.47        19.82        34.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            0.95             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           25.05           149.16 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
          15.040           45.005 
[1] "0.9 - 25.1 (15.0)"  "0.1 - 149.2 (45.0)"
[1] "hr="     "1200000"
D11V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NUDT11 MUTATED         1        0         2        1
  NUDT11 WILD-TYPE     207       43       110       71
D11V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                1              207
  STAGE II               0               43
  STAGE III              2              110
  STAGE IV               1               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUDT11 MUTATED     1   0   3   0
  NUDT11 WILD-TYPE 212  54 159   7
D11V4, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T1              1              212
  T2              0               54
  T3              3              159
  T4              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   1
  NUDT11 WILD-TYPE 204  14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    1
  NUDT11 WILD-TYPE  204   14
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              0              204
  1              1               14
[1] 2 2
[1] FALSE
D11V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     4   0
  NUDT11 WILD-TYPE 362  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      4    0
  NUDT11 WILD-TYPE  362   70
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              4              362
  1              0               70
[1] 2 2
[1] FALSE
D11V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   4
  NUDT11 WILD-TYPE 155 277
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    4
  NUDT11 WILD-TYPE  155  277
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              0              155
  MALE                4              277
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1               36 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-AK-3428       TCGA-AK-3430 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5843       TCGA-B4-5844 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-5456       TCGA-CZ-5457 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
D11V9, continuous
D11V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED       0                         0     4
  NUDT11 WILD-TYPE     6                        20   401
D11V11, multiclass
                           clus
vv                          NUDT11 MUTATED NUDT11 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0               20
  WHITE                                  4              401
[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"
D11V12, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   3
  NUDT11 WILD-TYPE  21 285
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    3
  NUDT11 WILD-TYPE   21  285
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0               21
  NOT HISPANIC OR LATINO              3              285
[1] 2 2
[1] FALSE

Clustering(12) Variable = PIK3CA MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     7   3
  PIK3CA WILD-TYPE 277 149
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              10              426 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               3              149 
$`PIK3CA MUTATED`
TCGA-BP-4160 TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-5713 TCGA-B8-5159 TCGA-BP-4352 
       94.72        88.37         2.53        91.46        23.74        11.31 
TCGA-BP-4960 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 
       71.41        74.27        64.18         7.36 

$`PIK3CA WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
      111.02        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       12.13        40.70         1.41         4.57         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-3924 
      130.65        79.89       131.15        89.49        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 
       45.37        17.19        25.55        50.14        40.04        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       49.84        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 
       10.98        36.95         6.71        47.97        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        79.66        47.18        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83       113.46        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
      119.64        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           94.72           149.16 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          67.795           44.055 
[1] "2.5 - 94.7 (67.8)"  "0.1 - 149.2 (44.1)"
[1] "hr=" "1.4"
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         2        2         4        2
  PIK3CA WILD-TYPE     206       41       108       70
D12V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                2              206
  STAGE II               2               41
  STAGE III              4              108
  STAGE IV               2               70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     2   2   6   0
  PIK3CA WILD-TYPE 211  52 156   7
D12V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              2              211
  T2              2               52
  T3              6              156
  T4              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     9   0
  PIK3CA WILD-TYPE 195  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      9    0
  PIK3CA WILD-TYPE  195   15
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              9              195
  1              0               15
[1] 2 2
[1] FALSE
D12V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   2
  PIK3CA WILD-TYPE 358  68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    2
  PIK3CA WILD-TYPE  358   68
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              8              358
  1              2               68
[1] 2 2
[1] FALSE
D12V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7   3
  PIK3CA WILD-TYPE 148 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    3
  PIK3CA WILD-TYPE  148  278
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              7              148
  MALE                3              278
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         0    10
  PIK3CA WILD-TYPE     6                        20   395
D12V11, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0               20
  WHITE                                 10              395
[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"
D12V12, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1   8
  PIK3CA WILD-TYPE  20 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    8
  PIK3CA WILD-TYPE   20  280
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               20
  NOT HISPANIC OR LATINO              8              280
[1] 2 2
[1] FALSE

Clustering(13) Variable = GPR50 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  GPR50 MUTATED     1   2
  GPR50 WILD-TYPE 283 150
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             433 
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             150 
$`GPR50 MUTATED`
TCGA-DV-5575 TCGA-DV-5576 TCGA-B0-4817 
       56.84        23.90        33.50 

$`GPR50 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       11.67        66.28        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       45.07        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  GPR50 MUTATED GPR50 WILD-TYPE 
          23.90            0.07 
  GPR50 MUTATED GPR50 WILD-TYPE 
          56.84          149.16 
  GPR50 MUTATED GPR50 WILD-TYPE 
          33.50           44.55 
[1] "23.9 - 56.8 (33.5)" "0.1 - 149.2 (44.5)"
[1] "hr=" "2.2"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GPR50 MUTATED         2        0         1        0
  GPR50 WILD-TYPE     206       43       111       72
D13V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE I               2             206
  STAGE II              0              43
  STAGE III             1             111
  STAGE IV              0              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  GPR50 MUTATED     2   0   1   0
  GPR50 WILD-TYPE 211  54 161   7
D13V4, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  T1             2             211
  T2             0              54
  T3             1             161
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                 cls
clus                0   1
  GPR50 MUTATED     1   0
  GPR50 WILD-TYPE 203  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    0
  GPR50 WILD-TYPE  203   15
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             1             203
  1             0              15
[1] 2 2
[1] FALSE
D13V6, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   0
  GPR50 WILD-TYPE 363  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    0
  GPR50 WILD-TYPE  363   70
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3             363
  1             0              70
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  GPR50 MUTATED     2   1
  GPR50 WILD-TYPE 153 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      2    1
  GPR50 WILD-TYPE  153  280
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             2             153
  MALE               1             280
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              2              35 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3428      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4858 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      TCGA-EU-5904 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
D13V9, continuous
D13V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED       0                         1     2
  GPR50 WILD-TYPE     6                        19   403
D13V11, multiclass
                           clus
vv                          GPR50 MUTATED GPR50 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1              19
  WHITE                                 2             403
[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"
D13V12, binary
                 cls
clus                0   1
  GPR50 MUTATED     0   3
  GPR50 WILD-TYPE  21 285
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    3
  GPR50 WILD-TYPE   21  285
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             3             285
[1] 2 2
[1] FALSE

Clustering(14) Variable = TFDP2 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2               0   1
  TFDP2 MUTATED     3   1
  TFDP2 WILD-TYPE 281 151
  TFDP2 MUTATED TFDP2 WILD-TYPE 
              4             432 
  TFDP2 MUTATED TFDP2 WILD-TYPE 
              1             151 
$`TFDP2 MUTATED`
TCGA-A3-3373 TCGA-BP-4338 TCGA-BP-4761 TCGA-CJ-4913 
       53.29        93.99         5.98        38.56 

$`TFDP2 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 
       45.53        88.37        51.25        74.63        74.76        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       72.59        77.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        49.28        50.33        54.48        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  TFDP2 MUTATED TFDP2 WILD-TYPE 
           5.98            0.07 
  TFDP2 MUTATED TFDP2 WILD-TYPE 
          93.99          149.16 
  TFDP2 MUTATED TFDP2 WILD-TYPE 
         45.925          44.350 
[1] "6.0 - 94.0 (45.9)"  "0.1 - 149.2 (44.3)"
[1] "hr=" "1.5"
D14V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TFDP2 MUTATED         2        0         2        0
  TFDP2 WILD-TYPE     206       43       110       72
D14V3, multiclass
           clus
vv          TFDP2 MUTATED TFDP2 WILD-TYPE
  STAGE I               2             206
  STAGE II              0              43
  STAGE III             2             110
  STAGE IV              0              72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TFDP2 MUTATED     2   0   2   0
  TFDP2 WILD-TYPE 211  54 160   7
D14V4, multiclass
    clus
vv   TFDP2 MUTATED TFDP2 WILD-TYPE
  T1             2             211
  T2             0              54
  T3             2             160
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                 cls
clus                0   1
  TFDP2 MUTATED     2   1
  TFDP2 WILD-TYPE 202  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP2 MUTATED      2    1
  TFDP2 WILD-TYPE  202   14
   clus
vv  TFDP2 MUTATED TFDP2 WILD-TYPE
  0             2             202
  1             1              14
[1] 2 2
[1] FALSE
D14V6, binary
                 cls
clus                0   1
  TFDP2 MUTATED     4   0
  TFDP2 WILD-TYPE 362  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP2 MUTATED      4    0
  TFDP2 WILD-TYPE  362   70
   clus
vv  TFDP2 MUTATED TFDP2 WILD-TYPE
  0             4             362
  1             0              70
[1] 2 2
[1] FALSE
D14V7, binary
                 cls
clus                0   1
  TFDP2 MUTATED     2   2
  TFDP2 WILD-TYPE 153 279
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP2 MUTATED      2    2
  TFDP2 WILD-TYPE  153  279
        clus
vv       TFDP2 MUTATED TFDP2 WILD-TYPE
  FEMALE             2             153
  MALE               2             279
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
D14V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TFDP2 MUTATED       0                         0     4
  TFDP2 WILD-TYPE     6                        20   401
D14V11, multiclass
                           clus
vv                          TFDP2 MUTATED TFDP2 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             0              20
  WHITE                                 4             401
[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"
D14V12, binary
                 cls
clus                0   1
  TFDP2 MUTATED     0   2
  TFDP2 WILD-TYPE  21 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TFDP2 MUTATED      0    2
  TFDP2 WILD-TYPE   21  286
                        clus
vv                       TFDP2 MUTATED TFDP2 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             2             286
[1] 2 2
[1] FALSE

Clustering(15) Variable = FAM200A MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  FAM200A MUTATED     4   0
  FAM200A WILD-TYPE 280 152
  FAM200A MUTATED FAM200A WILD-TYPE 
                4               432 
  FAM200A MUTATED FAM200A WILD-TYPE 
                0               152 
$`FAM200A MUTATED`
TCGA-BP-4775 TCGA-B0-4710 TCGA-B8-4154 TCGA-BP-4162 
       60.59        57.70        45.37       101.06 

$`FAM200A WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       44.15        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 
        3.48        19.00        65.10         5.98         2.14         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       42.71        25.05        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       90.28        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  FAM200A MUTATED FAM200A WILD-TYPE 
            45.37              0.07 
  FAM200A MUTATED FAM200A WILD-TYPE 
           101.06            149.16 
  FAM200A MUTATED FAM200A WILD-TYPE 
           59.145            43.825 
[1] "45.4 - 101.1 (59.1)" "0.1 - 149.2 (43.8)" 
[1] "hr="     "9100000"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM200A MUTATED         3        0         1        0
  FAM200A WILD-TYPE     205       43       111       72
D15V3, multiclass
           clus
vv          FAM200A MUTATED FAM200A WILD-TYPE
  STAGE I                 3               205
  STAGE II                0                43
  STAGE III               1               111
  STAGE IV                0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  FAM200A MUTATED     3   0   1   0
  FAM200A WILD-TYPE 210  54 161   7
D15V4, multiclass
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  T1               3               210
  T2               0                54
  T3               1               161
  T4               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
                   cls
clus                  0   1
  FAM200A MUTATED     3   0
  FAM200A WILD-TYPE 201  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      3    0
  FAM200A WILD-TYPE  201   15
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               3               201
  1               0                15
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                  0   1
  FAM200A MUTATED     4   0
  FAM200A WILD-TYPE 362  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      4    0
  FAM200A WILD-TYPE  362   70
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               4               362
  1               0                70
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  FAM200A MUTATED     4   0
  FAM200A WILD-TYPE 151 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      4    0
  FAM200A WILD-TYPE  151  281
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  FEMALE               4               151
  MALE                 0               281
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM200A MUTATED       0                         0     4
  FAM200A WILD-TYPE     6                        20   401
D15V11, multiclass
                           clus
vv                          FAM200A MUTATED FAM200A WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                20
  WHITE                                   4               401
[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"
D15V12, binary
                   cls
clus                  0   1
  FAM200A MUTATED     0   2
  FAM200A WILD-TYPE  21 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      0    2
  FAM200A WILD-TYPE   21  286
                        clus
vv                       FAM200A MUTATED FAM200A WILD-TYPE
  HISPANIC OR LATINO                   0                21
  NOT HISPANIC OR LATINO               2               286
[1] 2 2
[1] FALSE

Clustering(16) Variable = DPCR1 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 281 149
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             430 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              3             149 
$`DPCR1 MUTATED`
TCGA-DV-5576 TCGA-B0-5080 TCGA-CW-5589 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 
       23.90        11.24        78.18       107.41        94.45         1.94 

$`DPCR1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       11.67        66.28        56.84        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5083 
       36.85        70.52        20.94        43.30        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       85.78        66.31        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        91.69        55.33        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           1.94            0.07 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         107.41          149.16 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          51.04           44.35 
[1] "1.9 - 107.4 (51.0)" "0.1 - 149.2 (44.3)"
[1] "hr=" "1.3"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DPCR1 MUTATED         3        0         0        3
  DPCR1 WILD-TYPE     205       43       112       69
D16V3, multiclass
           clus
vv          DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I               3             205
  STAGE II              0              43
  STAGE III             0             112
  STAGE IV              3              69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DPCR1 MUTATED     3   0   3   0
  DPCR1 WILD-TYPE 210  54 159   7
D16V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             3             210
  T2             0              54
  T3             3             159
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                 cls
clus                0   1
  DPCR1 MUTATED     1   0
  DPCR1 WILD-TYPE 203  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      1    0
  DPCR1 WILD-TYPE  203   15
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             1             203
  1             0              15
[1] 2 2
[1] FALSE
D16V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 363  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      3    3
  DPCR1 WILD-TYPE  363   67
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             3             363
  1             3              67
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     2   4
  DPCR1 WILD-TYPE 153 277
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      2    4
  DPCR1 WILD-TYPE  153  277
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             2             153
  MALE               4             277
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              36 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5575      TCGA-AK-3428      TCGA-AK-3430      TCGA-B0-4838 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
D16V9, continuous
D16V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED       0                         1     5
  DPCR1 WILD-TYPE     6                        19   400
D16V11, multiclass
                           clus
vv                          DPCR1 MUTATED DPCR1 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1              19
  WHITE                                 5             400
[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"
D16V12, binary
                 cls
clus                0   1
  DPCR1 MUTATED     0   6
  DPCR1 WILD-TYPE  21 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      0    6
  DPCR1 WILD-TYPE   21  282
                        clus
vv                       DPCR1 MUTATED DPCR1 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             6             282
[1] 2 2
[1] FALSE

Clustering(17) Variable = EGFR MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     2   4
  EGFR WILD-TYPE 282 148
  EGFR MUTATED EGFR WILD-TYPE 
             6            430 
  EGFR MUTATED EGFR WILD-TYPE 
             4            148 
$`EGFR MUTATED`
TCGA-B0-4849 TCGA-B0-5116 TCGA-B0-5713 TCGA-BP-4341 TCGA-BP-4354 TCGA-CJ-4868 
        2.27        41.88        91.46        52.24        33.99        21.24 

$`EGFR WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 
      123.09       130.65        79.89       131.15        89.49        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       11.31        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  EGFR MUTATED EGFR WILD-TYPE 
          2.27           0.07 
  EGFR MUTATED EGFR WILD-TYPE 
         91.46         149.16 
  EGFR MUTATED EGFR WILD-TYPE 
        37.935         44.745 
[1] "2.3 - 91.5 (37.9)"  "0.1 - 149.2 (44.7)"
[1] "hr=" "2.2"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EGFR MUTATED         0        0         4        2
  EGFR WILD-TYPE     208       43       108       70
D17V3, multiclass
           clus
vv          EGFR MUTATED EGFR WILD-TYPE
  STAGE I              0            208
  STAGE II             0             43
  STAGE III            4            108
  STAGE IV             2             70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED     0   0   5   1
  EGFR WILD-TYPE 213  54 157   6
D17V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            0            213
  T2            0             54
  T3            5            157
  T4            1              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                cls
clus               0   1
  EGFR MUTATED     3   1
  EGFR WILD-TYPE 201  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      3    1
  EGFR WILD-TYPE  201   14
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            3            201
  1            1             14
[1] 2 2
[1] FALSE
D17V6, binary
                cls
clus               0   1
  EGFR MUTATED     4   2
  EGFR WILD-TYPE 362  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      4    2
  EGFR WILD-TYPE  362   68
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            4            362
  1            2             68
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  EGFR MUTATED     1   5
  EGFR WILD-TYPE 154 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      1    5
  EGFR WILD-TYPE  154  276
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            1            154
  MALE              5            276
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED       0                         0     6
  EGFR WILD-TYPE     6                        20   399
D17V11, multiclass
                           clus
vv                          EGFR MUTATED EGFR WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0             20
  WHITE                                6            399
[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"
D17V12, binary
                cls
clus               0   1
  EGFR MUTATED     0   4
  EGFR WILD-TYPE  21 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0    4
  EGFR WILD-TYPE   21  284
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            4            284
[1] 2 2
[1] FALSE

Clustering(18) Variable = SH3KBP1 MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  SH3KBP1 MUTATED     2   1
  SH3KBP1 WILD-TYPE 282 151
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                3               433 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
                1               151 
$`SH3KBP1 MUTATED`
TCGA-A3-3367 TCGA-B0-4842 TCGA-BP-4330 
       74.63        56.68        62.07 

$`SH3KBP1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       45.53        88.37        51.25        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       54.90        53.42        27.78         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            56.68              0.07 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            74.63            149.16 
  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE 
            62.07             43.96 
[1] "56.7 - 74.6 (62.1)" "0.1 - 149.2 (44.0)"
[1] "hr=" "1.5"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SH3KBP1 MUTATED         1        0         2        0
  SH3KBP1 WILD-TYPE     207       43       110       72
D18V3, multiclass
           clus
vv          SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  STAGE I                 1               207
  STAGE II                0                43
  STAGE III               2               110
  STAGE IV                0                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SH3KBP1 MUTATED     1   0   2   0
  SH3KBP1 WILD-TYPE 212  54 160   7
D18V4, multiclass
    clus
vv   SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  T1               1               212
  T2               0                54
  T3               2               160
  T4               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     3   0
  SH3KBP1 WILD-TYPE 201  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      3    0
  SH3KBP1 WILD-TYPE  201   15
   clus
vv  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  0               3               201
  1               0                15
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     3   0
  SH3KBP1 WILD-TYPE 363  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      3    0
  SH3KBP1 WILD-TYPE  363   70
   clus
vv  SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  0               3               363
  1               0                70
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     2   1
  SH3KBP1 WILD-TYPE 153 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      2    1
  SH3KBP1 WILD-TYPE  153  280
        clus
vv       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  FEMALE               2               153
  MALE                 1               280
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SH3KBP1 MUTATED       0                         1     2
  SH3KBP1 WILD-TYPE     6                        19   403
D18V11, multiclass
                           clus
vv                          SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               1                19
  WHITE                                   2               403
[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"
D18V12, binary
                   cls
clus                  0   1
  SH3KBP1 MUTATED     1   2
  SH3KBP1 WILD-TYPE  20 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SH3KBP1 MUTATED      1    2
  SH3KBP1 WILD-TYPE   20  286
                        clus
vv                       SH3KBP1 MUTATED SH3KBP1 WILD-TYPE
  HISPANIC OR LATINO                   1                20
  NOT HISPANIC OR LATINO               2               286
[1] 2 2
[1] FALSE

Clustering(19) Variable = EMG1 MUTATION ANALYSIS
D19V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 280 152
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            432 
  EMG1 MUTATED EMG1 WILD-TYPE 
             0            152 
$`EMG1 MUTATED`
TCGA-AK-3427 TCGA-AK-3440 TCGA-AS-3777 TCGA-BP-5186 
      117.80        94.19        40.70        22.78 

$`EMG1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3428 TCGA-AK-3429 
       43.20        55.76        65.52        20.28       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 
       15.78        73.68        68.61       109.51        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       12.13         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       37.22        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  EMG1 MUTATED EMG1 WILD-TYPE 
         22.78           0.07 
  EMG1 MUTATED EMG1 WILD-TYPE 
        117.80         149.16 
  EMG1 MUTATED EMG1 WILD-TYPE 
        67.445         44.350 
[1] "22.8 - 117.8 (67.4)" "0.1 - 149.2 (44.3)" 
[1] "hr="     "9100000"
D19V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EMG1 MUTATED         4        0         0        0
  EMG1 WILD-TYPE     204       43       112       72
D19V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              4            204
  STAGE II             0             43
  STAGE III            0            112
  STAGE IV             0             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EMG1 MUTATED     4   0   0   0
  EMG1 WILD-TYPE 209  54 162   7
D19V4, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T1            4            209
  T2            0             54
  T3            0            162
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                cls
clus               0   1
  EMG1 MUTATED     2   0
  EMG1 WILD-TYPE 202  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      2    0
  EMG1 WILD-TYPE  202   15
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            2            202
  1            0             15
[1] 2 2
[1] FALSE
D19V6, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 362  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  362   70
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            362
  1            0             70
[1] 2 2
[1] FALSE
D19V7, binary
                cls
clus               0   1
  EMG1 MUTATED     1   3
  EMG1 WILD-TYPE 154 278
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      1    3
  EMG1 WILD-TYPE  154  278
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            1            154
  MALE              3            278
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     4
  EMG1 WILD-TYPE     6                        20   401
D19V11, multiclass
                           clus
vv                          EMG1 MUTATED EMG1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0             20
  WHITE                                4            401
[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"
D19V12, binary
                cls
clus               0   1
  EMG1 MUTATED     0   3
  EMG1 WILD-TYPE  21 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    3
  EMG1 WILD-TYPE   21  285
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            3            285
[1] 2 2
[1] FALSE

Clustering(20) Variable = ARID1A MUTATION ANALYSIS
D20V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     6   4
  ARID1A WILD-TYPE 278 148
  ARID1A MUTATED ARID1A WILD-TYPE 
              10              426 
  ARID1A MUTATED ARID1A WILD-TYPE 
               4              148 
$`ARID1A MUTATED`
TCGA-BP-5199 TCGA-B0-5102 TCGA-B0-5692 TCGA-B0-5713 TCGA-B8-5549 TCGA-CJ-4912 
       44.55        90.87       129.67        91.46         6.38        54.48 
TCGA-CJ-6032 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4861 
      119.64        18.77        47.08        14.66 

$`ARID1A WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       46.39        56.98        42.41        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-3924 
      130.65        79.89       131.15        89.49        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        50.14        16.60        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       67.00        53.42        62.66         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4866 
       83.90        25.45        69.21        58.75        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.38             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          129.67           149.16 
  ARID1A MUTATED ARID1A WILD-TYPE 
          50.780           43.825 
[1] "6.4 - 129.7 (50.8)" "0.1 - 149.2 (43.8)"
[1] "hr=" "1.1"
D20V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         2        4         3        1
  ARID1A WILD-TYPE     206       39       109       71
D20V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                2              206
  STAGE II               4               39
  STAGE III              3              109
  STAGE IV               1               71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     2   4   4   0
  ARID1A WILD-TYPE 211  50 158   7
D20V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              2              211
  T2              4               50
  T3              4              158
  T4              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED     5   0
  ARID1A WILD-TYPE 199  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE  199   15
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              5              199
  1              0               15
[1] 2 2
[1] FALSE
D20V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED     9   1
  ARID1A WILD-TYPE 357  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      9    1
  ARID1A WILD-TYPE  357   69
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              9              357
  1              1               69
[1] 2 2
[1] FALSE
D20V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     4   6
  ARID1A WILD-TYPE 151 275
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      4    6
  ARID1A WILD-TYPE  151  275
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              4              151
  MALE                6              275
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               36 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-AK-3428       TCGA-AK-3430 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-5456       TCGA-CZ-5457 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D20V9, continuous
D20V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0    10
  ARID1A WILD-TYPE     6                        20   395
D20V11, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              0               20
  WHITE                                 10              395
[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"
D20V12, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2   6
  ARID1A WILD-TYPE  19 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    6
  ARID1A WILD-TYPE   19  282
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2               19
  NOT HISPANIC OR LATINO              6              282
[1] 2 2
[1] FALSE

Clustering(21) Variable = ARAP3 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 282 151
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             433 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             151 
$`ARAP3 MUTATED`
TCGA-A3-3323 TCGA-B0-4819 TCGA-CJ-4870 
       36.36         6.02        49.25 

$`ARAP3 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       49.02        48.59        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4822 TCGA-B0-4823 
        5.52        45.07        33.50        16.77        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 
       54.61        58.95        11.05        21.24        83.97        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           6.02            0.07 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          49.25          149.16 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          36.36           44.55 
[1] "6.0 - 49.2 (36.4)"  "0.1 - 149.2 (44.5)"
[1] "hr=" "1.4"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ARAP3 MUTATED         1        0         1        1
  ARAP3 WILD-TYPE     207       43       111       71
D21V3, multiclass
           clus
vv          ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I               1             207
  STAGE II              0              43
  STAGE III             1             111
  STAGE IV              1              71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  ARAP3 MUTATED     1   0   2   0
  ARAP3 WILD-TYPE 212  54 160   7
D21V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1             212
  T2             0              54
  T3             2             160
  T4             0               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   0
  ARAP3 WILD-TYPE 204  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    0
  ARAP3 WILD-TYPE  204   15
D21V6, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 364  69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  364   69
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0             2             364
  1             1              69
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 153 280
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  153  280
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE             2             153
  MALE               1             280
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED       0                         1     2
  ARAP3 WILD-TYPE     6                        19   403
D21V11, multiclass
                           clus
vv                          ARAP3 MUTATED ARAP3 WILD-TYPE
  ASIAN                                 0               6
  BLACK OR AFRICAN AMERICAN             1              19
  WHITE                                 2             403
[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"
D21V12, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   2
  ARAP3 WILD-TYPE  21 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    2
  ARAP3 WILD-TYPE   21  286
                        clus
vv                       ARAP3 MUTATED ARAP3 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             2             286
[1] 2 2
[1] FALSE

Clustering(22) Variable = SLC16A9 MUTATION ANALYSIS
D22V1, survival
                   sevent
clus2                 0   1
  SLC16A9 MUTATED     2   2
  SLC16A9 WILD-TYPE 282 150
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
                4               432 
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
                2               150 
$`SLC16A9 MUTATED`
TCGA-DV-5574 TCGA-B0-4818 TCGA-B2-4099 TCGA-CJ-5681 
       66.28        16.77        31.96        18.15 

$`SLC16A9 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       11.67        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
        5.52        45.07        33.50         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       32.61        35.90         1.68        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      133.71        25.71        18.87        22.32        25.25       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
            16.77              0.07 
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
            66.28            149.16 
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
           25.055            44.745 
[1] "16.8 - 66.3 (25.1)" "0.1 - 149.2 (44.7)"
[1] "hr=" "2"  
D22V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC16A9 MUTATED         2        1         0        1
  SLC16A9 WILD-TYPE     206       42       112       71
D22V3, multiclass
           clus
vv          SLC16A9 MUTATED SLC16A9 WILD-TYPE
  STAGE I                 2               206
  STAGE II                1                42
  STAGE III               0               112
  STAGE IV                1                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC16A9 MUTATED     2   1   1   0
  SLC16A9 WILD-TYPE 211  53 161   7
D22V4, multiclass
    clus
vv   SLC16A9 MUTATED SLC16A9 WILD-TYPE
  T1               2               211
  T2               1                53
  T3               1               161
  T4               0                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                   cls
clus                  0   1
  SLC16A9 MUTATED     0   0
  SLC16A9 WILD-TYPE 204  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A9 MUTATED      0    0
  SLC16A9 WILD-TYPE  204   15
D22V6, binary
                   cls
clus                  0   1
  SLC16A9 MUTATED     3   1
  SLC16A9 WILD-TYPE 363  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A9 MUTATED      3    1
  SLC16A9 WILD-TYPE  363   69
   clus
vv  SLC16A9 MUTATED SLC16A9 WILD-TYPE
  0               3               363
  1               1                69
[1] 2 2
[1] FALSE
D22V7, binary
                   cls
clus                  0   1
  SLC16A9 MUTATED     2   2
  SLC16A9 WILD-TYPE 153 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A9 MUTATED      2    2
  SLC16A9 WILD-TYPE  153  279
        clus
vv       SLC16A9 MUTATED SLC16A9 WILD-TYPE
  FEMALE               2               153
  MALE                 2               279
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "SLC16A9 MUTATED"       
clus
  SLC16A9 MUTATED SLC16A9 WILD-TYPE 
                1                36 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5575 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-DV-5576        TCGA-AK-3428        TCGA-AK-3430        TCGA-B0-4838 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-5456        TCGA-CZ-5457 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" "SLC16A9 WILD-TYPE" 
D22V9, continuous
D22V10, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC16A9 MUTATED       0                         0     4
  SLC16A9 WILD-TYPE     6                        20   401
D22V11, multiclass
                           clus
vv                          SLC16A9 MUTATED SLC16A9 WILD-TYPE
  ASIAN                                   0                 6
  BLACK OR AFRICAN AMERICAN               0                20
  WHITE                                   4               401
[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"
D22V12, binary
                   cls
clus                  0   1
  SLC16A9 MUTATED     0   4
  SLC16A9 WILD-TYPE  21 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A9 MUTATED      0    4
  SLC16A9 WILD-TYPE   21  284
                        clus
vv                       SLC16A9 MUTATED SLC16A9 WILD-TYPE
  HISPANIC OR LATINO                   0                21
  NOT HISPANIC OR LATINO               4               284
[1] 2 2
[1] FALSE

Clustering(23) Variable = PCK1 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     4   0
  PCK1 WILD-TYPE 280 152
  PCK1 MUTATED PCK1 WILD-TYPE 
             4            432 
  PCK1 MUTATED PCK1 WILD-TYPE 
             0            152 
$`PCK1 MUTATED`
TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 
       37.38       109.41        51.02        49.97 

$`PCK1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       49.02        48.59        36.36        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       55.76        65.52        20.28       117.80       122.56        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        52.87        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4905 
      109.84        50.24        56.35        47.67        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  PCK1 MUTATED PCK1 WILD-TYPE 
         37.38           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
        109.41         149.16 
  PCK1 MUTATED PCK1 WILD-TYPE 
        50.495         44.055 
[1] "37.4 - 109.4 (50.5)" "0.1 - 149.2 (44.1)" 
[1] "hr="     "9100000"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         2        1         1        0
  PCK1 WILD-TYPE     206       42       111       72
D23V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              2            206
  STAGE II             1             42
  STAGE III            1            111
  STAGE IV             0             72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PCK1 MUTATED     2   1   1   0
  PCK1 WILD-TYPE 211  53 161   7
D23V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            2            211
  T2            1             53
  T3            1            161
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                cls
clus               0   1
  PCK1 MUTATED     2   0
  PCK1 WILD-TYPE 202  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    0
  PCK1 WILD-TYPE  202   15
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            2            202
  1            0             15
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus               0   1
  PCK1 MUTATED     4   0
  PCK1 WILD-TYPE 362  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      4    0
  PCK1 WILD-TYPE  362   70
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            4            362
  1            0             70
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  PCK1 MUTATED     2   2
  PCK1 WILD-TYPE 153 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    2
  PCK1 WILD-TYPE  153  279
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            2            153
  MALE              2            279
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
D23V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED       0                         0     4
  PCK1 WILD-TYPE     6                        20   401
D23V11, multiclass
                           clus
vv                          PCK1 MUTATED PCK1 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0             20
  WHITE                                4            401
[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"
D23V12, binary
                cls
clus               0   1
  PCK1 MUTATED     0   3
  PCK1 WILD-TYPE  21 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    3
  PCK1 WILD-TYPE   21  285
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            3            285
[1] 2 2
[1] FALSE

Clustering(24) Variable = CUL9 MUTATION ANALYSIS
D24V1, survival
                sevent
clus2              0   1
  CUL9 MUTATED     5   2
  CUL9 WILD-TYPE 279 150
  CUL9 MUTATED CUL9 WILD-TYPE 
             7            429 
  CUL9 MUTATED CUL9 WILD-TYPE 
             2            150 
$`CUL9 MUTATED`
TCGA-AK-3428 TCGA-AK-3460 TCGA-B0-4697 TCGA-B0-5106 TCGA-BP-4761 TCGA-CJ-6032 
      122.56        82.45        19.00        52.54         5.98       119.64 
TCGA-CZ-5457 
       90.54 

$`CUL9 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 
       11.67        66.28        56.84        23.90        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3429 
       43.20        55.76        65.52        20.28       117.80       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 
       78.64        94.29        83.21        37.58        38.40        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       52.08        15.95        62.89        90.87        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        53.42        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  CUL9 MUTATED CUL9 WILD-TYPE 
          5.98           0.07 
  CUL9 MUTATED CUL9 WILD-TYPE 
        122.56         149.16 
  CUL9 MUTATED CUL9 WILD-TYPE 
         82.45          43.96 
[1] "6.0 - 122.6 (82.5)" "0.1 - 149.2 (44.0)"
[1] "hr=" "1.8"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CUL9 MUTATED         2        1         3        1
  CUL9 WILD-TYPE     206       42       109       71
D24V3, multiclass
           clus
vv          CUL9 MUTATED CUL9 WILD-TYPE
  STAGE I              2            206
  STAGE II             1             42
  STAGE III            3            109
  STAGE IV             1             71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  CUL9 MUTATED     2   1   4   0
  CUL9 WILD-TYPE 211  53 158   7
D24V4, multiclass
    clus
vv   CUL9 MUTATED CUL9 WILD-TYPE
  T1            2            211
  T2            1             53
  T3            4            158
  T4            0              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                cls
clus               0   1
  CUL9 MUTATED     2   1
  CUL9 WILD-TYPE 202  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL9 MUTATED      2    1
  CUL9 WILD-TYPE  202   14
   clus
vv  CUL9 MUTATED CUL9 WILD-TYPE
  0            2            202
  1            1             14
[1] 2 2
[1] FALSE
D24V6, binary
                cls
clus               0   1
  CUL9 MUTATED     6   1
  CUL9 WILD-TYPE 360  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL9 MUTATED      6    1
  CUL9 WILD-TYPE  360   69
   clus
vv  CUL9 MUTATED CUL9 WILD-TYPE
  0            6            360
  1            1             69
[1] 2 2
[1] FALSE
D24V7, binary
                cls
clus               0   1
  CUL9 MUTATED     2   5
  CUL9 WILD-TYPE 153 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL9 MUTATED      2    5
  CUL9 WILD-TYPE  153  276
        clus
vv       CUL9 MUTATED CUL9 WILD-TYPE
  FEMALE            2            153
  MALE              5            276
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "CUL9 MUTATED"          
clus
  CUL9 MUTATED CUL9 WILD-TYPE 
             2             35 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-AK-3430     TCGA-B0-4838 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-B8-4143     TCGA-B8-4622     TCGA-B8-5158     TCGA-CJ-6028 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-5456     TCGA-CZ-5458 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-EU-5904 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5906     TCGA-EU-5907 
"CUL9 WILD-TYPE" "CUL9 WILD-TYPE" "CUL9 WILD-TYPE" 
D24V9, continuous
D24V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CUL9 MUTATED       0                         0     7
  CUL9 WILD-TYPE     6                        20   398
D24V11, multiclass
                           clus
vv                          CUL9 MUTATED CUL9 WILD-TYPE
  ASIAN                                0              6
  BLACK OR AFRICAN AMERICAN            0             20
  WHITE                                7            398
[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"
D24V12, binary
                cls
clus               0   1
  CUL9 MUTATED     1   5
  CUL9 WILD-TYPE  20 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL9 MUTATED      1    5
  CUL9 WILD-TYPE   20  283
                        clus
vv                       CUL9 MUTATED CUL9 WILD-TYPE
  HISPANIC OR LATINO                1             20
  NOT HISPANIC OR LATINO            5            283
[1] 2 2
[1] FALSE

Clustering(25) Variable = ZDHHC1 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  ZDHHC1 MUTATED     4   0
  ZDHHC1 WILD-TYPE 280 152
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
               4              432 
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
               0              152 
$`ZDHHC1 MUTATED`
TCGA-B8-4621 TCGA-BP-4174 TCGA-CJ-4876 TCGA-CJ-4897 
       25.91        61.78        64.27       109.84 

$`ZDHHC1 WILD-TYPE`
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4158 
       70.68       119.38       126.05        24.82         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       66.28        56.84        23.90        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       79.66        47.18        74.27        75.06       116.84        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 

  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
           25.91             0.07 
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
          109.84           149.16 
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
          63.025           44.055 
[1] "25.9 - 109.8 (63.0)" "0.1 - 149.2 (44.1)" 
[1] "hr="     "9100000"
D25V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZDHHC1 MUTATED         1        2         1        0
  ZDHHC1 WILD-TYPE     207       41       111       72
D25V3, multiclass
           clus
vv          ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  STAGE I                1              207
  STAGE II               2               41
  STAGE III              1              111
  STAGE IV               0               72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZDHHC1 MUTATED     1   2   1   0
  ZDHHC1 WILD-TYPE 212  52 161   7
D25V4, multiclass
    clus
vv   ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  T1              1              212
  T2              2               52
  T3              1              161
  T4              0                7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                  cls
clus                 0   1
  ZDHHC1 MUTATED     3   0
  ZDHHC1 WILD-TYPE 201  15
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC1 MUTATED      3    0
  ZDHHC1 WILD-TYPE  201   15
   clus
vv  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  0              3              201
  1              0               15
[1] 2 2
[1] FALSE
D25V6, binary
                  cls
clus                 0   1
  ZDHHC1 MUTATED     4   0
  ZDHHC1 WILD-TYPE 362  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC1 MUTATED      4    0
  ZDHHC1 WILD-TYPE  362   70
   clus
vv  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  0              4              362
  1              0               70
[1] 2 2
[1] FALSE
D25V7, binary
                  cls
clus                 0   1
  ZDHHC1 MUTATED     1   3
  ZDHHC1 WILD-TYPE 154 278
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC1 MUTATED      1    3
  ZDHHC1 WILD-TYPE  154  278
        clus
vv       ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  FEMALE              1              154
  MALE                3              278
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
[1] "Remove cluster labels:" "ZDHHC1 MUTATED"        
clus
  ZDHHC1 MUTATED ZDHHC1 WILD-TYPE 
               1                6 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158 
"ZDHHC1 WILD-TYPE" "ZDHHC1 WILD-TYPE" "ZDHHC1 WILD-TYPE" "ZDHHC1 WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5550 
"ZDHHC1 WILD-TYPE" "ZDHHC1 WILD-TYPE" 
D25V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZDHHC1 MUTATED       0                         1     3
  ZDHHC1 WILD-TYPE     6                        19   402
D25V11, multiclass
                           clus
vv                          ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  ASIAN                                  0                6
  BLACK OR AFRICAN AMERICAN              1               19
  WHITE                                  3              402
[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"
D25V12, binary
                  cls
clus                 0   1
  ZDHHC1 MUTATED     2   1
  ZDHHC1 WILD-TYPE  19 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZDHHC1 MUTATED      2    1
  ZDHHC1 WILD-TYPE   19  287
                        clus
vv                       ZDHHC1 MUTATED ZDHHC1 WILD-TYPE
  HISPANIC OR LATINO                  2               19
  NOT HISPANIC OR LATINO              1              287
[1] 2 2
[1] FALSE
