[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/15081616/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/15182434/transformed.cor.cli.txt"

nPatients in clinical file=533, in cluster file=515, common to both=441
[1]  30 441
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             46             395 
  SETD2 MUTATED SETD2 WILD-TYPE 
             46             395 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            44            397 
  BAP1 MUTATED BAP1 WILD-TYPE 
            44            397 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            139             302 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            139             302 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             414 
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             414 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          171           270 
  VHL MUTATED VHL WILD-TYPE 
          171           270 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            17            424 
  PTEN MUTATED PTEN WILD-TYPE 
            17            424 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            28            413 
  MTOR MUTATED MTOR WILD-TYPE 
            28            413 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            12            429 
  TP53 MUTATED TP53 WILD-TYPE 
            12            429 
[1] "FAM200A MUTATION ANALYSIS"
[1] 3
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               436 
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               436 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             5            436 
  NEFH MUTATED NEFH WILD-TYPE 
             5            436 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             434 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             434 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            6           435 
  NF2 MUTATED NF2 WILD-TYPE 
            6           435 
[1] "CCDC120 MUTATION ANALYSIS"
[1] 3
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               437 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               437 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              429 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              429 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           12           429 
  ATM MUTATED ATM WILD-TYPE 
           12           429 
[1] "KIAA1751 MUTATION ANALYSIS"
[1] 3
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                435 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                435 
[1] "GUSB MUTATION ANALYSIS"
[1] 3
  GUSB MUTATED GUSB WILD-TYPE 
             4            437 
  GUSB MUTATED GUSB WILD-TYPE 
             4            437 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              430 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              430 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             438 
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             438 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            436 
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            436 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             435 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             435 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             435 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             435 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             7            434 
  EGFR MUTATED EGFR WILD-TYPE 
             7            434 
[1] "TRIM6 MUTATION ANALYSIS"
[1] 3
  TRIM6 MUTATED TRIM6 WILD-TYPE 
              5             436 
  TRIM6 MUTATED TRIM6 WILD-TYPE 
              5             436 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
             4            437 
  RBMX MUTATED RBMX WILD-TYPE 
             4            437 
[1] "GPR172B MUTATION ANALYSIS"
[1] 3
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               437 
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               437 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             437 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             437 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             438 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             438 
[1] "OPTC MUTATION ANALYSIS"
[1] 3
  OPTC MUTATED OPTC WILD-TYPE 
             4            437 
  OPTC MUTATED OPTC WILD-TYPE 
             4            437 
[1] "GOLGA5 MUTATION ANALYSIS"
[1] 3
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
               5              436 
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
               5              436 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 441 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=139,	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=289,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	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:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'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 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "440"  
freq.contrast "440"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "NUMBER_PACK_YEARS_SMOKED is excluded in the analysis because there is no more than two cases of (freq>=3) when the number of (unique non-NA values) is two"
            10      40     
freq.values "1"     "2"    
freq >=3    "FALSE" "FALSE"
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "YEAR_OF_TOBACCO_SMOKING_ONSET is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 441 columns, 1 survival variables, and 9 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"              "NEOPLASM_DISEASESTAGE"      
[3] "PATHOLOGY_T_STAGE"           "PATHOLOGY_N_STAGE"          
[5] "PATHOLOGY_M_STAGE"           "GENDER"                     
[7] "KARNOFSKY_PERFORMANCE_SCORE" "RACE"                       
[9] "ETHNICITY"                  
YEARS_TO_BIRTH, nv=58, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, 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 
216  56 162   7 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
216  56 162   7 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
216  56 162   7 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
216  56 162   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
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    25  21
  SETD2 WILD-TYPE 270 125
  SETD2 MUTATED SETD2 WILD-TYPE 
             46             395 
  SETD2 MUTATED SETD2 WILD-TYPE 
             21             125 
$`SETD2 MUTATED`
TCGA-A3-3311 TCGA-A3-3358 TCGA-A3-3383 TCGA-AK-3431 TCGA-AK-3455 TCGA-B0-4703 
       39.16        42.97        28.31        60.92        22.45         5.98 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4822 
        3.16        43.96        20.25        46.59         5.52        36.53 
TCGA-B0-4837 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5098 TCGA-B0-5121 
       45.30        65.29        36.85        11.90        52.08        18.21 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5699 TCGA-B4-5835 TCGA-BP-4161 TCGA-BP-4329 
       21.44        14.76        90.12         0.53        90.28        27.78 
TCGA-BP-4343 TCGA-BP-4759 TCGA-BP-4774 TCGA-BP-4790 TCGA-BP-4983 TCGA-BP-5006 
       62.86        77.98        61.97        36.53        46.45        27.62 
TCGA-BP-5169 TCGA-BP-5178 TCGA-BP-5198 TCGA-CJ-4872 TCGA-CJ-4891 TCGA-CJ-5671 
        6.35        62.86        19.82        47.18        26.93        63.88 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5580 TCGA-CW-5591 
       84.66        18.87        61.91        73.35        64.57        74.66 
TCGA-CZ-4861 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5470 
       14.66        55.33        10.85        12.69 

$`SETD2 WILD-TYPE`
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       52.93        45.53        88.37        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       15.78        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        45.93        28.73        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 
        4.57         2.53         3.48        19.00        65.10         2.14 
TCGA-B0-4707 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 
       19.73         6.64         3.25        15.72         0.59        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77         6.02        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       29.10        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        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        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       37.22       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       56.78        60.33        84.92        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.23         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        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        94.72       101.06        93.34        32.61        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-4331 TCGA-BP-4337 
       64.27        54.90        53.42        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        74.17        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 
       71.80        48.07        13.15        10.82         5.33        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4795 
       56.91        68.38        11.64        15.78        48.95        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        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        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       63.98        68.55        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        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        79.89 
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-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 
       92.02        81.83        85.78        66.31        78.18         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       47.08        69.21        58.75        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       56.28        55.33        56.94        47.01        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        31.10        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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.53            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
          90.28          120.59 
  SETD2 MUTATED SETD2 WILD-TYPE 
         38.005          37.580 
[1] "0.5 - 90.3 (38.0)"  "0.1 - 120.6 (37.6)"
[1] "hr=" "1.5"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        17        5        13       11
  SETD2 WILD-TYPE     194       40       102       59
D1V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              17             194
  STAGE II              5              40
  STAGE III            13             102
  STAGE IV             11              59
[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    18   6  20   2
  SETD2 WILD-TYPE 198  50 142   5
D1V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            18             198
  T2             6              50
  T3            20             142
  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  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     22    0
  SETD2 WILD-TYPE  182   16
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            22             182
  1             0              16
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    36  10
  SETD2 WILD-TYPE 335  60
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     36   10
  SETD2 WILD-TYPE  335   60
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            36             335
  1            10              60
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    13  33
  SETD2 WILD-TYPE 142 253
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     13   33
  SETD2 WILD-TYPE  142  253
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            13             142
  MALE              33             253
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              2              28 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5465 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED       1                         2    41
  SETD2 WILD-TYPE     6                        17   368
D1V9, multiclass
                           clus
vv                          SETD2 MUTATED SETD2 WILD-TYPE
  ASIAN                                 1               6
  BLACK OR AFRICAN AMERICAN             2              17
  WHITE                                41             368
[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"
D1V10, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  30
  SETD2 WILD-TYPE  21 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   30
  SETD2 WILD-TYPE   21  259
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              21
  NOT HISPANIC OR LATINO            30             259
[1] 2 2
[1] FALSE

Clustering(2) Variable = BAP1 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    20  24
  BAP1 WILD-TYPE 275 122
  BAP1 MUTATED BAP1 WILD-TYPE 
            44            397 
  BAP1 MUTATED BAP1 WILD-TYPE 
            24            122 
$`BAP1 MUTATED`
TCGA-A3-3317 TCGA-AK-3451 TCGA-B0-4691 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4713 
       49.02        48.69         4.57         5.98        19.73         6.64 
TCGA-B0-4827 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       29.10        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5107 TCGA-B0-5699 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4151 TCGA-B8-5551 
       30.48        90.12         5.46        23.31        27.55         0.53 
TCGA-BP-4163 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4798 
       93.34         0.07        18.48        11.31        31.33        10.98 
TCGA-BP-4962 TCGA-BP-5174 TCGA-BP-5182 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       58.68        74.20        38.30        63.25        73.22        14.17 
TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4923 
       54.61        83.97        74.27        66.21        61.91        18.81 
TCGA-CJ-5680 TCGA-CW-5580 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5469 
       25.25        64.57        18.77        61.41        58.82        31.10 
TCGA-CZ-5470 TCGA-CZ-5985 
       12.69        65.65 

$`BAP1 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.08        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 
       57.37        46.78        42.08        58.49        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         1.41         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 
       65.10         2.14         3.16        43.96         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       10.95        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 
       46.68        56.78        60.33        84.92        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         0.23         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        0.23        16.80        27.16        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       14.27        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        32.61        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-4331 TCGA-BP-4338 TCGA-BP-4341 
       53.42        27.78        62.07        80.68        93.99        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       31.89        33.99        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        60.30        61.22        61.51         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         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 
       28.87        48.10         6.35        79.30         1.78        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
       52.27         9.63        62.86        74.40        49.15        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       75.88        65.69        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06        77.36        64.27        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 
       84.66        25.71        18.87        22.32        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       62.66        83.77         7.36        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 
       14.66        60.59        63.39         5.46        63.42         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40         1.94        80.19        67.96        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.07           0.23 
  BAP1 MUTATED BAP1 WILD-TYPE 
         93.34         120.59 
  BAP1 MUTATED BAP1 WILD-TYPE 
        28.325         39.160 
[1] "0.1 - 93.3 (28.3)"  "0.2 - 120.6 (39.2)"
[1] "hr=" "2"  
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BAP1 MUTATED         7        7        18       12
  BAP1 WILD-TYPE     204       38        97       58
D2V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              7            204
  STAGE II             7             38
  STAGE III           18             97
  STAGE IV            12             58
[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
  BAP1 MUTATED     8  11  25   0
  BAP1 WILD-TYPE 208  45 137   7
D2V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            8            208
  T2           11             45
  T3           25            137
  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
  BAP1 MUTATED    26   4
  BAP1 WILD-TYPE 178  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     26    4
  BAP1 WILD-TYPE  178   12
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           26            178
  1            4             12
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  BAP1 MUTATED    31  13
  BAP1 WILD-TYPE 340  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     31   13
  BAP1 WILD-TYPE  340   57
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           31            340
  1           13             57
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  BAP1 MUTATED    24  20
  BAP1 WILD-TYPE 131 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     24   20
  BAP1 WILD-TYPE  131  266
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE           24            131
  MALE             20            266
[1] 2 2
[1] FALSE
D2V8, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             28 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5843 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5907 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED       0                         2    40
  BAP1 WILD-TYPE     7                        17   369
D2V9, multiclass
                           clus
vv                          BAP1 MUTATED BAP1 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            2             17
  WHITE                               40            369
[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"
D2V10, binary
                cls
clus               0   1
  BAP1 MUTATED     3  32
  BAP1 WILD-TYPE  19 257
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3   32
  BAP1 WILD-TYPE   19  257
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                3             19
  NOT HISPANIC OR LATINO           32            257
[1] 2 2
[1] FALSE

Clustering(3) Variable = PBRM1 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    95  44
  PBRM1 WILD-TYPE 200 102
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            139             302 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             44             102 
$`PBRM1 MUTATED`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.08        48.59        36.36        37.38        48.82 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3431 
       51.25        74.63        53.29        20.28       109.91        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4706 
       68.61        67.20        42.08        38.40        31.27         2.14 
TCGA-B0-4718 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4822 TCGA-B0-4824 
       20.25        52.21        45.07        16.77        36.53        54.48 
TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.09        56.68        65.29        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        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5693 
       11.80        26.20        21.60        16.21        21.44       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 
       15.78        46.68        56.78        84.92        90.12        39.55 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4099 
      120.59        47.97        96.36        89.49        61.32        12.30 
TCGA-B2-4101 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4148 
       21.30         9.57         0.23         4.64         0.23        27.16 
TCGA-B8-4154 TCGA-B8-5158 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4176 
       24.66        20.91       111.02        85.51        32.61        64.27 
TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4759 TCGA-BP-4774 TCGA-BP-4801 
       27.78         0.07        52.24        77.98        61.97        36.95 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4981 
        6.71        71.41        61.22        45.50        47.11        36.07 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4993 
       33.34        31.30        36.95        27.22         3.88         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 
       45.07        41.62        48.10         6.35        79.30        74.40 
TCGA-BP-5181 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5198 
       49.15        37.25        22.78        13.35        27.02        19.82 
TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 
       34.95        59.84        46.55        11.05        79.66        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4903 TCGA-CJ-4905 
       77.36        57.83        30.64        51.52        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5676 
       50.33        54.48        38.56         4.57        18.81        84.66 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6030 TCGA-CJ-6033 
       18.87        22.32        61.91        73.35        75.58         7.36 
TCGA-CW-5580 TCGA-CW-5589 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-5453 
       64.57        78.18       103.43        25.45        46.16         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 
       23.74        18.44        56.28        47.01        10.85        47.54 
TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
       22.52        12.69        80.19        12.26        62.63        45.96 
TCGA-EU-5907 
        4.18 

$`PBRM1 WILD-TYPE`
TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3363 
       49.02        52.93        45.53        88.37        42.97        10.49 
TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       28.70        74.76        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3440 
       65.52        84.36        73.08        66.31        15.78        57.37 
TCGA-AK-3443 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       46.78        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       37.58        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        4.57         2.53         3.48        19.00        65.10         5.98 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
       19.73         3.16        43.96         6.64         3.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4823 
       46.59         0.59         5.52        33.50         6.02        14.93 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4945 
        6.71        11.64        10.29        39.45        29.03        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-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        15.09         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5117 
       62.89        90.87        52.54        29.95        19.30        17.59 
TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
        1.94        18.21        37.22        14.76       112.80        48.89 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       60.33        56.94        52.77        79.36        92.98       102.48 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 
       97.41        32.61        35.90         1.68        11.77        10.36 
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-B8-4621 
       16.80        27.55        25.05        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        94.72        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-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4340 
       54.90        53.42        62.07        80.68        93.99        18.48 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 
       10.98        37.25        47.97         6.94        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 
       49.38         7.23        53.65        14.93        46.45        25.81 
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-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       38.30        42.44        37.22        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
       13.41        24.62        33.47        44.55        31.27         0.95 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
       58.95        21.24        83.97        49.25        74.27        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        69.86        64.18 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 
       58.92        49.28        45.14         3.06        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 
       79.89        25.71        25.25        18.15        62.10        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       60.99        53.42        62.66        83.77        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-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5457 
       63.39         5.46        61.41        63.42        58.82        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5468 
       56.94        55.33        10.22        21.76         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 
       31.10        67.96        65.65        14.63        22.78        43.69 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 
        3.91         6.77 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.36 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         120.59          112.80 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         39.160          37.235 
[1] "0.1 - 120.6 (39.2)" "0.4 - 112.8 (37.2)"
[1] "hr=" "1.1"
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        67       15        35       22
  PBRM1 WILD-TYPE     144       30        80       48
D3V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              67             144
  STAGE II             15              30
  STAGE III            35              80
  STAGE IV             22              48
[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    68  22  49   0
  PBRM1 WILD-TYPE 148  34 113   7
D3V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            68             148
  T2            22              34
  T3            49             113
  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
  PBRM1 MUTATED    61   2
  PBRM1 WILD-TYPE 143  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     61    2
  PBRM1 WILD-TYPE  143   14
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0            61             143
  1             2              14
[1] 2 2
[1] FALSE
D3V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   116  23
  PBRM1 WILD-TYPE 255  47
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    116   23
  PBRM1 WILD-TYPE  255   47
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0           116             255
  1            23              47
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    46  93
  PBRM1 WILD-TYPE 109 193
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     46   93
  PBRM1 WILD-TYPE  109  193
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            46             109
  MALE              93             193
[1] 2 2
[1] FALSE
D3V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       1                         3   131
  PBRM1 WILD-TYPE     6                        16   278
D3V9, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 1               6
  BLACK OR AFRICAN AMERICAN             3              16
  WHITE                               131             278
[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"
D3V10, binary
                 cls
clus                0   1
  PBRM1 MUTATED     4  92
  PBRM1 WILD-TYPE  18 197
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4   92
  PBRM1 WILD-TYPE   18  197
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 4              18
  NOT HISPANIC OR LATINO            92             197
[1] 2 2
[1] FALSE

Clustering(4) Variable = KDM5C MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    14  13
  KDM5C WILD-TYPE 281 133
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             414 
  KDM5C MUTATED KDM5C WILD-TYPE 
             13             133 
$`KDM5C MUTATED`
TCGA-A3-3331 TCGA-AK-3430 TCGA-AK-3458 TCGA-B0-4694 TCGA-B0-4718 TCGA-B0-4816 
       48.82        15.78        38.40         3.48        20.25        45.07 
TCGA-B0-4828 TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5106 
       10.09        45.30        10.29        43.30        10.95        52.54 
TCGA-B0-5108 TCGA-B0-5698 TCGA-B2-5641 TCGA-BP-4159 TCGA-BP-4342 TCGA-BP-4351 
       29.95        84.92        21.57        85.51        74.17        31.89 
TCGA-BP-4803 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5202 
        6.71        18.51         6.35        27.02        33.24         0.95 
TCGA-CJ-4871 TCGA-CW-5581 TCGA-CZ-5467 
       79.66        92.02         2.40 

$`KDM5C WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       73.08        66.31        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       22.45        37.58        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 
        1.41         1.41         4.57         2.53        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        15.72        46.59         0.59         5.52        52.21 
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-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       29.10        78.44        40.70        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 
        2.27        36.85        70.52        20.94        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 
       34.36         7.30        25.32        18.51        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        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       46.68        56.78        60.33        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B4-5377 
        1.68        12.30        21.30        11.77        10.36         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
      111.02        94.72        90.28       101.06        93.34        32.61 
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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       80.68         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-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         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         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
        5.82        43.00        45.07        30.64        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        47.18        74.27        75.06        77.36 
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        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 
       62.66        83.77         7.36        64.57        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        47.54        22.52         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
          92.02          120.59 
  KDM5C MUTATED KDM5C WILD-TYPE 
          29.95           38.63 
[1] "0.9 - 92.0 (29.9)"  "0.1 - 120.6 (38.6)"
[1] "hr=" "1.7"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        13        2         8        4
  KDM5C WILD-TYPE     198       43       107       66
D4V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              13             198
  STAGE II              2              43
  STAGE III             8             107
  STAGE IV              4              66
[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   3  11   0
  KDM5C WILD-TYPE 203  53 151   7
D4V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            13             203
  T2             3              53
  T3            11             151
  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"
D4V5, binary
                 cls
clus                0   1
  KDM5C MUTATED    14   1
  KDM5C WILD-TYPE 190  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     14    1
  KDM5C WILD-TYPE  190   15
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            14             190
  1             1              15
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    23   4
  KDM5C WILD-TYPE 348  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     23    4
  KDM5C WILD-TYPE  348   66
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            23             348
  1             4              66
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     3  24
  KDM5C WILD-TYPE 152 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      3   24
  KDM5C WILD-TYPE  152  262
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             3             152
  MALE              24             262
[1] 2 2
[1] FALSE
D4V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              29 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      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-EU-5904      TCGA-EU-5905 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EU-5907 
"KDM5C WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED       0                         1    26
  KDM5C WILD-TYPE     7                        18   383
D4V9, multiclass
                           clus
vv                          KDM5C MUTATED KDM5C WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              18
  WHITE                                26             383
[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"
D4V10, binary
                 cls
clus                0   1
  KDM5C MUTATED     0  20
  KDM5C WILD-TYPE  22 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   20
  KDM5C WILD-TYPE   22  269
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO            20             269
[1] 2 2
[1] FALSE

Clustering(5) Variable = VHL MUTATION ANALYSIS
D5V1, survival
               sevent
clus2             0   1
  VHL MUTATED   117  54
  VHL WILD-TYPE 178  92
  VHL MUTATED VHL WILD-TYPE 
          171           270 
  VHL MUTATED VHL WILD-TYPE 
           54            92 
$`VHL MUTATED`
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 
       48.82        45.53        51.25        53.29        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3455 TCGA-AK-3458 TCGA-AS-3778 TCGA-B0-4700 
       28.31        65.52        22.45        38.40         1.41        65.10 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4814 
        2.14        19.73        43.96         6.64        15.72         5.52 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4842 
       16.77         6.02        14.93        29.10        10.09        56.68 
TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 
       26.07        36.85        70.52        43.30        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5102 
       18.51         8.05         2.24        21.86        15.95        90.87 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5402 
       52.54        30.48        29.95        11.80        26.20        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5703 
      112.80        48.89       101.13        46.68        56.78        39.55 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
      120.59       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-5635 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4148 
       35.90        10.36         0.23         4.64         0.36        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       27.55        25.05        24.66        23.74         1.18        27.02 
TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4167 
       24.23         6.38         0.53        85.51        32.61        89.36 
TCGA-BP-4329 TCGA-BP-4341 TCGA-BP-4771 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       27.78        52.24         5.33         6.94        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 
        7.23        47.11        53.65        14.93        33.34        25.81 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-4998 
       27.22         3.88        46.45        16.47        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       36.23         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        49.15        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-BP-5199 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82        44.55        59.84        63.25        73.22        14.17 
TCGA-CJ-4644 TCGA-CJ-4875 TCGA-CJ-4894 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4908 
       11.05        77.36        27.65        56.35        51.29        50.33 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5672 TCGA-CJ-5676 
       54.48        45.14         3.06         4.57        72.00        84.66 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6030 
       25.71        25.25        73.35        67.00        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5588 
       62.66        83.77         7.36        64.57        81.83        66.31 
TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4861 
       74.66        83.90       103.43        25.45         0.59        14.66 
TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       56.94        47.01        47.54        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-EU-5904 
       67.96        65.65        12.26        14.63        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

$`VHL WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       52.93        88.37        42.97        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       74.76        43.20        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       37.58        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4710 
        4.57         2.53         3.48        19.00         5.98         3.16 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        3.25        20.25        46.59         0.59        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       33.50        36.53        54.48        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        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5083 
       39.45        29.03         2.27        20.94        11.24        34.36 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 
        7.30        15.09        10.95        52.08        62.89        90.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       19.30        35.90        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 
       18.21        21.44        37.22        15.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5712 
       90.12        56.94        52.77        79.36        92.98        89.49 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       32.61         1.68        12.30        21.30        11.77        21.57 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 
        9.57         1.25         0.53         5.46         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       16.80        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
        0.85        17.16        16.60        14.27        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
      111.02        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 
       71.80        48.07        13.15        10.82        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4981 
       47.97        58.68        48.89        49.38        45.50        36.07 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 
       46.45        31.30        36.95         5.82        43.00        18.51 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5187 
       28.87        48.10        62.86        38.30        37.22        13.35 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 
       27.02        31.79        34.95        31.27         0.95        46.55 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
       75.88        65.69        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       49.25        79.66        47.18        74.27        75.06        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        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-4923 TCGA-CJ-5671 
       58.92        49.18        49.28        38.56        18.81        63.88 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       79.89        18.87        22.32        18.15        61.91        62.10 
TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6097 
       53.42        92.02        85.78        78.18         1.35        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16        47.08        69.21        58.75        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        56.28        55.33        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5988 TCGA-DV-5565 
       21.76        22.52         2.40         1.94        22.78        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 

  VHL MUTATED VHL WILD-TYPE 
         0.23          0.07 
  VHL MUTATED VHL WILD-TYPE 
       120.59        111.02 
  VHL MUTATED VHL WILD-TYPE 
       33.470        41.225 
[1] "0.2 - 120.6 (33.5)" "0.1 - 111.0 (41.2)"
[1] "hr=" "1"  
D5V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED        93       13        42       23
  VHL WILD-TYPE     118       32        73       47
D5V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I            93           118
  STAGE II           13            32
  STAGE III          42            73
  STAGE IV           23            47
[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    94  17  56   4
  VHL WILD-TYPE 122  39 106   3
D5V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1          94           122
  T2          17            39
  T3          56           106
  T4           4             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
               cls
clus              0   1
  VHL MUTATED    75   5
  VHL WILD-TYPE 129  11
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     75    5
  VHL WILD-TYPE  129   11
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0          75           129
  1           5            11
[1] 2 2
[1] FALSE
D5V6, binary
               cls
clus              0   1
  VHL MUTATED   148  23
  VHL WILD-TYPE 223  47
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    148   23
  VHL WILD-TYPE  223   47
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0         148           223
  1          23            47
[1] 2 2
[1] FALSE
D5V7, binary
               cls
clus              0   1
  VHL MUTATED    64 107
  VHL WILD-TYPE  91 179
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     64  107
  VHL WILD-TYPE   91  179
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          64            91
  MALE           107           179
[1] 2 2
[1] FALSE
D5V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED       2                         2   164
  VHL WILD-TYPE     5                        17   245
D5V9, multiclass
                           clus
vv                          VHL MUTATED VHL WILD-TYPE
  ASIAN                               2             5
  BLACK OR AFRICAN AMERICAN           2            17
  WHITE                             164           245
[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"
D5V10, binary
               cls
clus              0   1
  VHL MUTATED     9 109
  VHL WILD-TYPE  13 180
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      9  109
  VHL WILD-TYPE   13  180
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               9            13
  NOT HISPANIC OR LATINO         109           180
[1] 2 2
[1] FALSE

Clustering(6) Variable = PTEN MUTATION ANALYSIS
D6V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    11   6
  PTEN WILD-TYPE 284 140
  PTEN MUTATED PTEN WILD-TYPE 
            17            424 
  PTEN MUTATED PTEN WILD-TYPE 
             6            140 
$`PTEN MUTATED`
TCGA-A3-3316 TCGA-AK-3427 TCGA-B0-4694 TCGA-B0-4810 TCGA-B0-4843 TCGA-B8-4621 
       49.08        84.36         3.48        15.72        11.64        25.91 
TCGA-B8-5158 TCGA-BP-4161 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4351 TCGA-BP-5010 
       20.91        90.28        53.42        49.84        31.89        28.87 
TCGA-BP-5199 TCGA-CJ-4871 TCGA-CZ-4858 TCGA-DV-5568 TCGA-EU-5907 
       44.55        79.66        69.21        12.16         4.18 

$`PTEN WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.64        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       40.70         1.41         1.41         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        20.25        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        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-B0-4844 
       45.30        27.42        53.88         6.71        56.68        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-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        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        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       92.98       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       25.55        23.01        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       34.39        14.30       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        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-4329 
       77.03        62.24        61.78        64.27        54.90        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       74.17        62.86        49.08        44.94        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
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-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       24.62        33.47        19.82        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        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        77.36        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        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66        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        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         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-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
       18.77        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       62.63        43.69        45.96        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       23.90        18.12         3.91         6.77 

  PTEN MUTATED PTEN WILD-TYPE 
          3.48           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         90.28         120.59 
  PTEN MUTATED PTEN WILD-TYPE 
         31.89          37.94 
[1] "3.5 - 90.3 (31.9)"  "0.1 - 120.6 (37.9)"
[1] "hr=" "1.1"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         5        3         8        1
  PTEN WILD-TYPE     206       42       107       69
D6V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              5            206
  STAGE II             3             42
  STAGE III            8            107
  STAGE IV             1             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
  PTEN MUTATED     5   3   9   0
  PTEN WILD-TYPE 211  53 153   7
D6V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            5            211
  T2            3             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"
D6V5, binary
                cls
clus               0   1
  PTEN MUTATED     8   2
  PTEN WILD-TYPE 196  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8    2
  PTEN WILD-TYPE  196   14
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            8            196
  1            2             14
[1] 2 2
[1] FALSE
D6V6, binary
                cls
clus               0   1
  PTEN MUTATED    16   1
  PTEN WILD-TYPE 355  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     16    1
  PTEN WILD-TYPE  355   69
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           16            355
  1            1             69
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus               0   1
  PTEN MUTATED     2  15
  PTEN WILD-TYPE 153 271
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2   15
  PTEN WILD-TYPE  153  271
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            2            153
  MALE             15            271
[1] 2 2
[1] FALSE
D6V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         1    16
  PTEN WILD-TYPE     7                        18   393
D6V9, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            1             18
  WHITE                               16            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"
D6V10, binary
                cls
clus               0   1
  PTEN MUTATED     0  13
  PTEN WILD-TYPE  22 276
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   13
  PTEN WILD-TYPE   22  276
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO           13            276
[1] 2 2
[1] FALSE

Clustering(7) Variable = MTOR MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    14  14
  MTOR WILD-TYPE 281 132
  MTOR MUTATED MTOR WILD-TYPE 
            28            413 
  MTOR MUTATED MTOR WILD-TYPE 
            14            132 
$`MTOR MUTATED`
TCGA-A3-3347 TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 TCGA-B0-4846 TCGA-B0-4852 
       52.93        66.31        15.72        29.10        39.45        36.85 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5691 TCGA-B0-5696 TCGA-B0-5697 
       52.08        62.89         1.94       112.80        56.78        60.33 
TCGA-B0-5701 TCGA-B0-5712 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-BP-5175 
       56.94        89.49         0.23         4.64         0.23        30.64 
TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4887 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-6027 
       52.27        11.05        30.64        49.28        22.32        60.99 
TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5987 
       64.57        47.08        61.41        14.63 

$`MTOR WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       48.82        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       73.08        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        20.25        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       36.53        14.93        54.48        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        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        65.29        26.07        29.03         2.27        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-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       17.59        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 
       48.89       101.13        15.78        46.68        84.92        90.12 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       47.97        96.36        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 
        9.57         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        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        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-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        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-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
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-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
        1.78        74.20         9.63        62.86        74.40        49.15 
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-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       65.69        54.61        58.95        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        77.36        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        69.86        64.18 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       72.00        79.89        84.66        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15        61.91        62.10        73.35        67.00        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66        83.77         7.36        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-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
      103.43        18.77        25.45        46.16         0.59        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 
       58.75        14.66        60.59        63.39         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  MTOR MUTATED MTOR WILD-TYPE 
          0.23           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        112.80         120.59 
  MTOR MUTATED MTOR WILD-TYPE 
         48.18          37.38 
[1] "0.2 - 112.8 (48.2)" "0.1 - 120.6 (37.4)"
[1] "hr=" "1.5"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED         9        3         9        7
  MTOR WILD-TYPE     202       42       106       63
D7V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I              9            202
  STAGE II             3             42
  STAGE III            9            106
  STAGE IV             7             63
[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 206  52 148   7
D7V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1           10            206
  T2            4             52
  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"
D7V5, binary
                cls
clus               0   1
  MTOR MUTATED    15   2
  MTOR WILD-TYPE 189  14
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     15    2
  MTOR WILD-TYPE  189   14
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           15            189
  1            2             14
[1] 2 2
[1] FALSE
D7V6, binary
                cls
clus               0   1
  MTOR MUTATED    21   7
  MTOR WILD-TYPE 350  63
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     21    7
  MTOR WILD-TYPE  350   63
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           21            350
  1            7             63
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  MTOR MUTATED    14  14
  MTOR WILD-TYPE 141 272
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     14   14
  MTOR WILD-TYPE  141  272
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           14            141
  MALE             14            272
[1] 2 2
[1] FALSE
D7V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED       0                         3    25
  MTOR WILD-TYPE     7                        16   384
D7V9, multiclass
                           clus
vv                          MTOR MUTATED MTOR WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            3             16
  WHITE                               25            384
[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"
D7V10, binary
                cls
clus               0   1
  MTOR MUTATED     1  25
  MTOR WILD-TYPE  21 264
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   25
  MTOR WILD-TYPE   21  264
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             21
  NOT HISPANIC OR LATINO           25            264
[1] 2 2
[1] FALSE

Clustering(8) Variable = TP53 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     5   7
  TP53 WILD-TYPE 290 139
  TP53 MUTATED TP53 WILD-TYPE 
            12            429 
  TP53 MUTATED TP53 WILD-TYPE 
             7            139 
$`TP53 MUTATED`
TCGA-AK-3440 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-5098 TCGA-B0-5117 TCGA-BP-4176 
       57.37         5.98         3.16        52.08        17.59        64.27 
TCGA-BP-4770 TCGA-BP-4798 TCGA-CJ-5677 TCGA-CZ-4858 TCGA-CZ-4865 TCGA-CZ-5463 
       10.82        10.98        25.71        69.21         5.46        21.76 

$`TP53 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       67.20        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 
        3.48        19.00        65.10         2.14        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        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 
       11.64        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-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        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        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       92.98       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        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-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        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-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 
       44.15        41.75        71.80        48.07        13.15         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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        77.36        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        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        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-5678 
       18.81        63.88        72.00        79.89        84.66        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        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
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-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45        46.16         0.59        47.08        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       60.59        63.39        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       47.01        10.85        10.22        47.54        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-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  TP53 MUTATED TP53 WILD-TYPE 
          3.16           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
         69.21         120.59 
  TP53 MUTATED TP53 WILD-TYPE 
        19.675         38.400 
[1] "3.2 - 69.2 (19.7)"  "0.1 - 120.6 (38.4)"
[1] "hr=" "2.6"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         5        2         2        3
  TP53 WILD-TYPE     206       43       113       67
D8V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              5            206
  STAGE II             2             43
  STAGE III            2            113
  STAGE IV             3             67
[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   2   4   1
  TP53 WILD-TYPE 211  54 158   6
D8V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            5            211
  T2            2             54
  T3            4            158
  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"
D8V5, binary
                cls
clus               0   1
  TP53 MUTATED     4   0
  TP53 WILD-TYPE 200  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4    0
  TP53 WILD-TYPE  200   16
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            4            200
  1            0             16
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus               0   1
  TP53 MUTATED     9   3
  TP53 WILD-TYPE 362  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9    3
  TP53 WILD-TYPE  362   67
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            9            362
  1            3             67
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  TP53 MUTATED     5   7
  TP53 WILD-TYPE 150 279
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      5    7
  TP53 WILD-TYPE  150  279
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            5            150
  MALE              7            279
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             29 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EU-5907 
"TP53 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         1    11
  TP53 WILD-TYPE     7                        18   398
D8V9, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            1             18
  WHITE                               11            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"
D8V10, binary
                cls
clus               0   1
  TP53 MUTATED     0   8
  TP53 WILD-TYPE  22 281
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    8
  TP53 WILD-TYPE   22  281
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            8            281
[1] 2 2
[1] FALSE

Clustering(9) Variable = FAM200A MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 291 145
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               436 
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               145 
$`FAM200A MUTATED`
TCGA-B0-4710 TCGA-B8-4154 TCGA-BP-4162 TCGA-BP-4762 TCGA-BP-4775 
        3.16        24.66       101.06        44.15        60.59 

$`FAM200A WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       19.73        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       27.55        25.05        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       14.30       111.02        85.51        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         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-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
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-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        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        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        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-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  FAM200A MUTATED FAM200A WILD-TYPE 
             3.16              0.07 
  FAM200A MUTATED FAM200A WILD-TYPE 
           101.06            120.59 
  FAM200A MUTATED FAM200A WILD-TYPE 
            44.15             37.53 
[1] "3.2 - 101.1 (44.1)" "0.1 - 120.6 (37.5)"
[1] "hr=" "2"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM200A MUTATED         4        0         1        0
  FAM200A WILD-TYPE     207       45       114       70
D9V3, multiclass
           clus
vv          FAM200A MUTATED FAM200A WILD-TYPE
  STAGE I                 4               207
  STAGE II                0                45
  STAGE III               1               114
  STAGE IV                0                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
  FAM200A MUTATED     4   0   1   0
  FAM200A WILD-TYPE 212  56 161   7
D9V4, multiclass
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  T1               4               212
  T2               0                56
  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"
D9V5, binary
                   cls
clus                  0   1
  FAM200A MUTATED     3   0
  FAM200A WILD-TYPE 201  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      3    0
  FAM200A WILD-TYPE  201   16
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               3               201
  1               0                16
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                  0   1
  FAM200A MUTATED     5   0
  FAM200A WILD-TYPE 366  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      5    0
  FAM200A WILD-TYPE  366   70
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               5               366
  1               0                70
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 151 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      4    1
  FAM200A WILD-TYPE  151  285
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  FEMALE               4               151
  MALE                 1               285
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM200A MUTATED       0                         0     5
  FAM200A WILD-TYPE     7                        19   404
D9V9, multiclass
                           clus
vv                          FAM200A MUTATED FAM200A WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                19
  WHITE                                   5               404
[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"
D9V10, binary
                   cls
clus                  0   1
  FAM200A MUTATED     0   2
  FAM200A WILD-TYPE  22 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      0    2
  FAM200A WILD-TYPE   22  287
                        clus
vv                       FAM200A MUTATED FAM200A WILD-TYPE
  HISPANIC OR LATINO                   0                22
  NOT HISPANIC OR LATINO               2               287
[1] 2 2
[1] FALSE

Clustering(10) Variable = NEFH MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     3   2
  NEFH WILD-TYPE 292 144
  NEFH MUTATED NEFH WILD-TYPE 
             5            436 
  NEFH MUTATED NEFH WILD-TYPE 
             2            144 
$`NEFH MUTATED`
TCGA-AK-3451 TCGA-B0-4706 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CZ-5456 
       48.69         2.14        18.15        62.10        56.28 

$`NEFH WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3453 
       67.20        57.37        46.78        42.08        58.49        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 
        3.48        19.00        65.10         5.98        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         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        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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        77.36        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        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 
       18.87        22.32        25.25        61.91        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
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 
         62.10         120.59 
  NEFH MUTATED NEFH WILD-TYPE 
         48.69          37.53 
[1] "2.1 - 62.1 (48.7)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "1.4"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         1        2         1        1
  NEFH WILD-TYPE     210       43       114       69
D10V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              1            210
  STAGE II             2             43
  STAGE III            1            114
  STAGE IV             1             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
  NEFH MUTATED     1   2   2   0
  NEFH WILD-TYPE 215  54 160   7
D10V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            1            215
  T2            2             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"
D10V5, binary
                cls
clus               0   1
  NEFH MUTATED     2   0
  NEFH WILD-TYPE 202  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    0
  NEFH WILD-TYPE  202   16
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            2            202
  1            0             16
[1] 2 2
[1] FALSE
D10V6, binary
                cls
clus               0   1
  NEFH MUTATED     4   1
  NEFH WILD-TYPE 367  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    1
  NEFH WILD-TYPE  367   69
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            4            367
  1            1             69
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus               0   1
  NEFH MUTATED     1   4
  NEFH WILD-TYPE 154 282
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      1    4
  NEFH WILD-TYPE  154  282
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            1            154
  MALE              4            282
[1] 2 2
[1] FALSE
D10V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             29 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5457 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     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-EU-5904     TCGA-EU-5905 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-EU-5907 
"NEFH WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED       0                         0     5
  NEFH WILD-TYPE     7                        19   404
D10V9, multiclass
                           clus
vv                          NEFH MUTATED NEFH WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                5            404
[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"
D10V10, binary
                cls
clus               0   1
  NEFH MUTATED     0   4
  NEFH WILD-TYPE  22 285
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    4
  NEFH WILD-TYPE   22  285
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            4            285
[1] 2 2
[1] FALSE

Clustering(11) Variable = PTCH1 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED     4   3
  PTCH1 WILD-TYPE 291 143
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             434 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              3             143 
$`PTCH1 MUTATED`
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4814 TCGA-B8-4153 TCGA-BP-4337 TCGA-BP-4768 
        6.64        20.25         5.52        25.05         0.07        13.15 
TCGA-BP-4777 
       56.91 

$`PTCH1 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
       19.73         3.16        43.96         3.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59        52.21        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 
       11.64        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-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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-B8-4154 
        0.23        23.31        16.80        27.16        27.55        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
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-4331 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       80.68        93.99        18.48        52.24        74.17        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-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4770 
        5.98        44.15        41.75        71.80        48.07        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
        5.33        61.97        60.59        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         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         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
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-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        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        77.36 
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        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 
        6.77         4.18 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.07            0.23 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          56.91          120.59 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          13.15           38.48 
[1] "0.1 - 56.9 (13.2)"  "0.2 - 120.6 (38.5)"
[1] "hr=" "2.9"
D11V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTCH1 MUTATED         2        0         4        1
  PTCH1 WILD-TYPE     209       45       111       69
D11V3, multiclass
           clus
vv          PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I               2             209
  STAGE II              0              45
  STAGE III             4             111
  STAGE IV              1              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
  PTCH1 MUTATED     2   0   4   1
  PTCH1 WILD-TYPE 214  56 158   6
D11V4, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             2             214
  T2             0              56
  T3             4             158
  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"
D11V5, binary
                 cls
clus                0   1
  PTCH1 MUTATED     3   0
  PTCH1 WILD-TYPE 201  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    0
  PTCH1 WILD-TYPE  201   16
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0             3             201
  1             0              16
[1] 2 2
[1] FALSE
D11V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED     6   1
  PTCH1 WILD-TYPE 365  69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      6    1
  PTCH1 WILD-TYPE  365   69
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0             6             365
  1             1              69
[1] 2 2
[1] FALSE
D11V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED     3   4
  PTCH1 WILD-TYPE 152 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    4
  PTCH1 WILD-TYPE  152  282
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE             3             152
  MALE               4             282
[1] 2 2
[1] FALSE
D11V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED       0                         0     7
  PTCH1 WILD-TYPE     7                        19   402
D11V9, multiclass
                           clus
vv                          PTCH1 MUTATED PTCH1 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              19
  WHITE                                 7             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"
D11V10, binary
                 cls
clus                0   1
  PTCH1 MUTATED     0   5
  PTCH1 WILD-TYPE  22 284
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      0    5
  PTCH1 WILD-TYPE   22  284
                        clus
vv                       PTCH1 MUTATED PTCH1 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             5             284
[1] 2 2
[1] FALSE

Clustering(12) Variable = NF2 MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  NF2 MUTATED     3   3
  NF2 WILD-TYPE 292 143
  NF2 MUTATED NF2 WILD-TYPE 
            6           435 
  NF2 MUTATED NF2 WILD-TYPE 
            3           143 
$`NF2 MUTATED`
TCGA-B0-5084 TCGA-B0-5098 TCGA-B8-4153 TCGA-BP-4986 TCGA-CJ-4638 TCGA-CJ-4901 
        7.30        52.08        25.05        25.81        14.17        47.67 

$`NF2 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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        11.64        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-B0-5085 
       20.94        43.30        11.24        11.90        34.36        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         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        27.16        27.55 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        31.30        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        56.35        49.97        51.29        58.92 
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        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         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-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  NF2 MUTATED NF2 WILD-TYPE 
         7.30          0.07 
  NF2 MUTATED NF2 WILD-TYPE 
        52.08        120.59 
  NF2 MUTATED NF2 WILD-TYPE 
        25.43         38.30 
[1] "7.3 - 52.1 (25.4)"  "0.1 - 120.6 (38.3)"
[1] "hr=" "2.3"
D12V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         2        2
  NF2 WILD-TYPE     209       45       113       68
D12V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2           209
  STAGE II            0            45
  STAGE III           2           113
  STAGE IV            2            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
  NF2 MUTATED     2   0   4   0
  NF2 WILD-TYPE 214  56 158   7
D12V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           2           214
  T2           0            56
  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"
D12V5, binary
               cls
clus              0   1
  NF2 MUTATED     1   2
  NF2 WILD-TYPE 203  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    2
  NF2 WILD-TYPE  203   14
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           1           203
  1           2            14
[1] 2 2
[1] FALSE
D12V6, binary
               cls
clus              0   1
  NF2 MUTATED     4   2
  NF2 WILD-TYPE 367  68
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      4    2
  NF2 WILD-TYPE  367   68
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           4           367
  1           2            68
[1] 2 2
[1] FALSE
D12V7, binary
               cls
clus              0   1
  NF2 MUTATED     2   4
  NF2 WILD-TYPE 153 282
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    4
  NF2 WILD-TYPE  153  282
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           2           153
  MALE             4           282
[1] 2 2
[1] FALSE
D12V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED       0                         1     5
  NF2 WILD-TYPE     7                        18   404
D12V9, multiclass
                           clus
vv                          NF2 MUTATED NF2 WILD-TYPE
  ASIAN                               0             7
  BLACK OR AFRICAN AMERICAN           1            18
  WHITE                               5           404
[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"
D12V10, binary
               cls
clus              0   1
  NF2 MUTATED     1   5
  NF2 WILD-TYPE  21 284
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1    5
  NF2 WILD-TYPE   21  284
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1            21
  NOT HISPANIC OR LATINO           5           284
[1] 2 2
[1] FALSE

Clustering(13) Variable = CCDC120 MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 291 146
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               437 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                0               146 
$`CCDC120 MUTATED`
TCGA-AK-3425 TCGA-BP-4759 TCGA-CJ-4876 TCGA-CZ-5470 
      109.91        77.98        64.27        12.69 

$`CCDC120 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       55.76        18.64        28.31        65.52        20.28        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.62         5.98        44.15        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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        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 
       63.88        72.00        79.89        84.66        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        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
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-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        31.10        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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  CCDC120 MUTATED CCDC120 WILD-TYPE 
            12.69              0.07 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           109.91            120.59 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           71.125            37.480 
[1] "12.7 - 109.9 (71.1)" "0.1 - 120.6 (37.5)" 
[1] "hr="     "9200000"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC120 MUTATED         2        2         0        0
  CCDC120 WILD-TYPE     209       43       115       70
D13V3, multiclass
           clus
vv          CCDC120 MUTATED CCDC120 WILD-TYPE
  STAGE I                 2               209
  STAGE II                2                43
  STAGE III               0               115
  STAGE IV                0                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
  CCDC120 MUTATED     2   2   0   0
  CCDC120 WILD-TYPE 214  54 162   7
D13V4, multiclass
    clus
vv   CCDC120 MUTATED CCDC120 WILD-TYPE
  T1               2               214
  T2               2                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"
D13V5, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     3   0
  CCDC120 WILD-TYPE 201  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      3    0
  CCDC120 WILD-TYPE  201   16
   clus
vv  CCDC120 MUTATED CCDC120 WILD-TYPE
  0               3               201
  1               0                16
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 367  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      4    0
  CCDC120 WILD-TYPE  367   70
   clus
vv  CCDC120 MUTATED CCDC120 WILD-TYPE
  0               4               367
  1               0                70
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     1   3
  CCDC120 WILD-TYPE 154 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    3
  CCDC120 WILD-TYPE  154  283
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  FEMALE               1               154
  MALE                 3               283
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC120 MUTATED       0                         0     3
  CCDC120 WILD-TYPE     7                        19   406
D13V9, multiclass
                           clus
vv                          CCDC120 MUTATED CCDC120 WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                19
  WHITE                                   3               406
[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"
D13V10, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     1   2
  CCDC120 WILD-TYPE  21 287
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    2
  CCDC120 WILD-TYPE   21  287
                        clus
vv                       CCDC120 MUTATED CCDC120 WILD-TYPE
  HISPANIC OR LATINO                   1                21
  NOT HISPANIC OR LATINO               2               287
[1] 2 2
[1] FALSE

Clustering(14) Variable = PIK3CA MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     8   4
  PIK3CA WILD-TYPE 287 142
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              429 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4              142 
$`PIK3CA MUTATED`
TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-4824 TCGA-B0-5713 TCGA-B8-5159 TCGA-BP-4160 
       88.37         2.53        54.48        61.32        23.74        94.72 
TCGA-BP-4352 TCGA-BP-4960 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 
       11.31        71.41        47.18        74.27        64.18         7.36 

$`PIK3CA WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       48.82        52.93        45.53        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       12.13        40.70         1.41         1.41         4.57         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
        6.02        36.53        14.93        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 
       11.64        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-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
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        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
       17.19        25.55        25.91        23.01        20.91         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        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-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97         6.94        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       79.66        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83        69.86        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        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        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        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-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       53.42        75.58        62.66        83.77        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-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           94.72           120.59 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           57.90            37.38 
[1] "2.5 - 94.7 (57.9)"  "0.1 - 120.6 (37.4)"
[1] "hr=" "1.3"
D14V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         4        2         4        2
  PIK3CA WILD-TYPE     207       43       111       68
D14V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                4              207
  STAGE II               2               43
  STAGE III              4              111
  STAGE IV               2               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
  PIK3CA MUTATED     4   2   6   0
  PIK3CA WILD-TYPE 212  54 156   7
D14V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              4              212
  T2              2               54
  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"
D14V5, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    11   0
  PIK3CA WILD-TYPE 193  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     11    0
  PIK3CA WILD-TYPE  193   16
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             11              193
  1              0               16
[1] 2 2
[1] FALSE
D14V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10   2
  PIK3CA WILD-TYPE 361  68
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    2
  PIK3CA WILD-TYPE  361   68
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             10              361
  1              2               68
[1] 2 2
[1] FALSE
D14V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   4
  PIK3CA WILD-TYPE 147 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    4
  PIK3CA WILD-TYPE  147  282
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              8              147
  MALE                4              282
[1] 2 2
[1] FALSE
D14V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         0    12
  PIK3CA WILD-TYPE     7                        19   397
D14V9, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              0               19
  WHITE                                 12              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"
D14V10, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  10
  PIK3CA WILD-TYPE  21 279
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   10
  PIK3CA WILD-TYPE   21  279
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               21
  NOT HISPANIC OR LATINO             10              279
[1] 2 2
[1] FALSE

Clustering(15) Variable = ATM MUTATION ANALYSIS
D15V1, survival
               sevent
clus2             0   1
  ATM MUTATED     8   4
  ATM WILD-TYPE 287 142
  ATM MUTATED ATM WILD-TYPE 
           12           429 
  ATM MUTATED ATM WILD-TYPE 
            4           142 
$`ATM MUTATED`
TCGA-B0-4690 TCGA-B0-5097 TCGA-B0-5703 TCGA-BP-4964 TCGA-BP-5173 TCGA-CJ-4639 
        1.41        21.86        39.55        61.22         1.78        75.88 
TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-5686 TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 
       56.35        58.92        67.00        14.66        63.42        12.26 

$`ATM WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       28.04        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-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       18.51        15.09        10.95         8.05         2.24        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       14.17        65.69        54.61        58.95        11.05        21.24 
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 
       77.36        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 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       50.24        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        63.88        72.00        79.89        84.66        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        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        60.99        53.42        75.58        62.66        83.77 
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-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5453 
       60.59        63.39         5.46        61.41        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  ATM MUTATED ATM WILD-TYPE 
         1.41          0.07 
  ATM MUTATED ATM WILD-TYPE 
        75.88        120.59 
  ATM MUTATED ATM WILD-TYPE 
        47.95         37.48 
[1] "1.4 - 75.9 (48.0)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "1"  
D15V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         5        3         1        3
  ATM WILD-TYPE     206       42       114       67
D15V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             5           206
  STAGE II            3            42
  STAGE III           1           114
  STAGE IV            3            67
[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   2   2
  ATM WILD-TYPE 211  53 160   5
D15V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           5           211
  T2           3            53
  T3           2           160
  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"
D15V5, binary
               cls
clus              0   1
  ATM MUTATED     7   2
  ATM WILD-TYPE 197  14
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      7    2
  ATM WILD-TYPE  197   14
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           7           197
  1           2            14
[1] 2 2
[1] FALSE
D15V6, binary
               cls
clus              0   1
  ATM MUTATED     9   3
  ATM WILD-TYPE 362  67
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      9    3
  ATM WILD-TYPE  362   67
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           9           362
  1           3            67
[1] 2 2
[1] FALSE
D15V7, binary
               cls
clus              0   1
  ATM MUTATED     6   6
  ATM WILD-TYPE 149 280
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      6    6
  ATM WILD-TYPE  149  280
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           6           149
  MALE             6           280
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            29 
   TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4862    TCGA-CZ-5456 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469    TCGA-CZ-5982    TCGA-DV-5565 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5907 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         0    12
  ATM WILD-TYPE     7                        19   397
D15V9, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             7
  BLACK OR AFRICAN AMERICAN           0            19
  WHITE                              12           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"
D15V10, binary
               cls
clus              0   1
  ATM MUTATED     1   6
  ATM WILD-TYPE  21 283
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    6
  ATM WILD-TYPE   21  283
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            21
  NOT HISPANIC OR LATINO           6           283
[1] 2 2
[1] FALSE

Clustering(16) Variable = KIAA1751 MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                  0   1
  KIAA1751 MUTATED     4   2
  KIAA1751 WILD-TYPE 291 144
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                435 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 2                144 
$`KIAA1751 MUTATED`
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3434 TCGA-B0-5703 TCGA-CZ-5467 TCGA-CZ-5984 
       73.08        15.78        68.61        39.55         2.40        67.96 

$`KIAA1751 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       84.36        66.31        60.92        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        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 
       11.64        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-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 
       60.33        84.92        90.12        56.94        52.77       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
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        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       22.52         1.94        31.10        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
              2.40               0.07 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
             73.08             120.59 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
            53.755             37.480 
[1] "2.4 - 73.1 (53.8)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "1.1"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1751 MUTATED         3        0         3        0
  KIAA1751 WILD-TYPE     208       45       112       70
D16V3, multiclass
           clus
vv          KIAA1751 MUTATED KIAA1751 WILD-TYPE
  STAGE I                  3                208
  STAGE II                 0                 45
  STAGE III                3                112
  STAGE IV                 0                 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
  KIAA1751 MUTATED     3   0   3   0
  KIAA1751 WILD-TYPE 213  56 159   7
D16V4, multiclass
    clus
vv   KIAA1751 MUTATED KIAA1751 WILD-TYPE
  T1                3                213
  T2                0                 56
  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
  KIAA1751 MUTATED     4   1
  KIAA1751 WILD-TYPE 200  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      4    1
  KIAA1751 WILD-TYPE  200   15
   clus
vv  KIAA1751 MUTATED KIAA1751 WILD-TYPE
  0                4                200
  1                1                 15
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     6   0
  KIAA1751 WILD-TYPE 365  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      6    0
  KIAA1751 WILD-TYPE  365   70
   clus
vv  KIAA1751 MUTATED KIAA1751 WILD-TYPE
  0                6                365
  1                0                 70
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     1   5
  KIAA1751 WILD-TYPE 154 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      1    5
  KIAA1751 WILD-TYPE  154  281
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  FEMALE                1                154
  MALE                  5                281
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "KIAA1751 MUTATED"      
clus
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 1                 29 
        TCGA-B0-4838         TCGA-B4-5377         TCGA-B4-5832 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4858 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-4862         TCGA-CZ-5456 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5465         TCGA-CZ-5469 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5574 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5907 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1751 MUTATED       0                         0     6
  KIAA1751 WILD-TYPE     7                        19   403
D16V9, multiclass
                           clus
vv                          KIAA1751 MUTATED KIAA1751 WILD-TYPE
  ASIAN                                    0                  7
  BLACK OR AFRICAN AMERICAN                0                 19
  WHITE                                    6                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"
D16V10, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     0   5
  KIAA1751 WILD-TYPE  22 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      0    5
  KIAA1751 WILD-TYPE   22  284
                        clus
vv                       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  HISPANIC OR LATINO                    0                 22
  NOT HISPANIC OR LATINO                5                284
[1] 2 2
[1] FALSE

Clustering(17) Variable = GUSB MUTATION ANALYSIS
D17V1, survival
                sevent
clus2              0   1
  GUSB MUTATED     2   2
  GUSB WILD-TYPE 293 144
  GUSB MUTATED GUSB WILD-TYPE 
             4            437 
  GUSB MUTATED GUSB WILD-TYPE 
             2            144 
$`GUSB MUTATED`
TCGA-B0-5095 TCGA-BP-4159 TCGA-CJ-4884 TCGA-CJ-4902 
        8.05        85.51        57.83        49.97 

$`GUSB WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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        11.64        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-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09        10.95         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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       34.39        14.30       111.02        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  GUSB MUTATED GUSB WILD-TYPE 
          8.05           0.07 
  GUSB MUTATED GUSB WILD-TYPE 
         85.51         120.59 
  GUSB MUTATED GUSB WILD-TYPE 
         53.90          37.48 
[1] "8.1 - 85.5 (53.9)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "1.2"
D17V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GUSB MUTATED         1        0         3        0
  GUSB WILD-TYPE     210       45       112       70
D17V3, multiclass
           clus
vv          GUSB MUTATED GUSB WILD-TYPE
  STAGE I              1            210
  STAGE II             0             45
  STAGE III            3            112
  STAGE IV             0             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
  GUSB MUTATED     1   0   3   0
  GUSB WILD-TYPE 215  56 159   7
D17V4, multiclass
    clus
vv   GUSB MUTATED GUSB WILD-TYPE
  T1            1            215
  T2            0             56
  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"
D17V5, binary
                cls
clus               0   1
  GUSB MUTATED     2   0
  GUSB WILD-TYPE 202  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      2    0
  GUSB WILD-TYPE  202   16
   clus
vv  GUSB MUTATED GUSB WILD-TYPE
  0            2            202
  1            0             16
[1] 2 2
[1] FALSE
D17V6, binary
                cls
clus               0   1
  GUSB MUTATED     4   0
  GUSB WILD-TYPE 367  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      4    0
  GUSB WILD-TYPE  367   70
   clus
vv  GUSB MUTATED GUSB WILD-TYPE
  0            4            367
  1            0             70
[1] 2 2
[1] FALSE
D17V7, binary
                cls
clus               0   1
  GUSB MUTATED     1   3
  GUSB WILD-TYPE 154 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      1    3
  GUSB WILD-TYPE  154  283
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  FEMALE            1            154
  MALE              3            283
[1] 2 2
[1] FALSE
D17V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUSB MUTATED       0                         0     4
  GUSB WILD-TYPE     7                        19   405
D17V9, multiclass
                           clus
vv                          GUSB MUTATED GUSB WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                4            405
[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"
D17V10, binary
                cls
clus               0   1
  GUSB MUTATED     0   3
  GUSB WILD-TYPE  22 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      0    3
  GUSB WILD-TYPE   22  286
                        clus
vv                       GUSB MUTATED GUSB WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            3            286
[1] 2 2
[1] FALSE

Clustering(18) Variable = ARID1A MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     7   4
  ARID1A WILD-TYPE 288 142
  ARID1A MUTATED ARID1A WILD-TYPE 
              11              430 
  ARID1A MUTATED ARID1A WILD-TYPE 
               4              142 
$`ARID1A MUTATED`
TCGA-B0-5102 TCGA-B0-5692 TCGA-B0-5713 TCGA-B8-5549 TCGA-BP-5199 TCGA-CJ-4892 
       90.87        48.89        61.32         6.38        44.55        50.01 
TCGA-CJ-4912 TCGA-CJ-6032 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4861 
       54.48        83.77        18.77        47.08        14.66 

$`ARID1A WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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        11.64        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-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       37.22        14.76       112.80       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       96.36        89.49        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
       16.60        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
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-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       68.55        26.93        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        49.28        50.33        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       62.66         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-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
       25.45        46.16         0.59        69.21        58.75        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.38             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
           90.87           120.59 
  ARID1A MUTATED ARID1A WILD-TYPE 
          48.890           37.315 
[1] "6.4 - 90.9 (48.9)"  "0.1 - 120.6 (37.3)"
[1] "hr=" "1.1"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         3        4         3        1
  ARID1A WILD-TYPE     208       41       112       69
D18V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                3              208
  STAGE II               4               41
  STAGE III              3              112
  STAGE IV               1               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
  ARID1A MUTATED     3   4   4   0
  ARID1A WILD-TYPE 213  52 158   7
D18V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              3              213
  T2              4               52
  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"
D18V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED     6   0
  ARID1A WILD-TYPE 198  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    0
  ARID1A WILD-TYPE  198   16
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              6              198
  1              0               16
[1] 2 2
[1] FALSE
D18V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    10   1
  ARID1A WILD-TYPE 361  69
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     10    1
  ARID1A WILD-TYPE  361   69
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             10              361
  1              1               69
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     5   6
  ARID1A WILD-TYPE 150 280
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    6
  ARID1A WILD-TYPE  150  280
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              5              150
  MALE                6              280
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               29 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982       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-EU-5904       TCGA-EU-5905 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EU-5907 
"ARID1A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0    11
  ARID1A WILD-TYPE     7                        19   398
D18V9, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              0               19
  WHITE                                 11              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"
D18V10, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2   7
  ARID1A WILD-TYPE  20 282
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    7
  ARID1A WILD-TYPE   20  282
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2               20
  NOT HISPANIC OR LATINO              7              282
[1] 2 2
[1] FALSE

Clustering(19) Variable = GPR50 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  GPR50 MUTATED     1   2
  GPR50 WILD-TYPE 294 144
  GPR50 MUTATED GPR50 WILD-TYPE 
              3             438 
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             144 
$`GPR50 MUTATED`
TCGA-B0-4817 TCGA-DV-5575 TCGA-DV-5576 
       33.50        56.84        23.90 

$`GPR50 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         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         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
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-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        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        77.36 
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        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       11.67        66.28        18.12         3.91         6.77         4.18 

  GPR50 MUTATED GPR50 WILD-TYPE 
          23.90            0.07 
  GPR50 MUTATED GPR50 WILD-TYPE 
          56.84          120.59 
  GPR50 MUTATED GPR50 WILD-TYPE 
          33.50           37.94 
[1] "23.9 - 56.8 (33.5)" "0.1 - 120.6 (37.9)"
[1] "hr=" "2.1"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GPR50 MUTATED         2        0         1        0
  GPR50 WILD-TYPE     209       45       114       70
D19V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE I               2             209
  STAGE II              0              45
  STAGE III             1             114
  STAGE IV              0              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
  GPR50 MUTATED     2   0   1   0
  GPR50 WILD-TYPE 214  56 161   7
D19V4, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  T1             2             214
  T2             0              56
  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"
D19V5, binary
                 cls
clus                0   1
  GPR50 MUTATED     1   0
  GPR50 WILD-TYPE 203  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      1    0
  GPR50 WILD-TYPE  203   16
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             1             203
  1             0              16
[1] 2 2
[1] FALSE
D19V6, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   0
  GPR50 WILD-TYPE 368  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    0
  GPR50 WILD-TYPE  368   70
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3             368
  1             0              70
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  GPR50 MUTATED     2   1
  GPR50 WILD-TYPE 153 285
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      2    1
  GPR50 WILD-TYPE  153  285
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             2             153
  MALE               1             285
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              2              28 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DV-5574      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED       0                         1     2
  GPR50 WILD-TYPE     7                        18   407
D19V9, multiclass
                           clus
vv                          GPR50 MUTATED GPR50 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              18
  WHITE                                 2             407
[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"
D19V10, binary
                 cls
clus                0   1
  GPR50 MUTATED     0   3
  GPR50 WILD-TYPE  22 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    3
  GPR50 WILD-TYPE   22  286
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             3             286
[1] 2 2
[1] FALSE

Clustering(20) Variable = PCK1 MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 290 146
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            436 
  PCK1 MUTATED PCK1 WILD-TYPE 
             0            146 
$`PCK1 MUTATED`
TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 TCGA-CZ-5456 
       37.38        66.31         1.94        49.97        56.28 

$`PCK1 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3331 
       39.16        49.08        49.02        48.59        36.36        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       73.08        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       17.59        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  PCK1 MUTATED PCK1 WILD-TYPE 
          1.94           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
         66.31         120.59 
  PCK1 MUTATED PCK1 WILD-TYPE 
         49.97          37.53 
[1] "1.9 - 66.3 (50.0)"  "0.1 - 120.6 (37.5)"
[1] "hr="     "9100000"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         2        2         1        0
  PCK1 WILD-TYPE     209       43       114       70
D20V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              2            209
  STAGE II             2             43
  STAGE III            1            114
  STAGE IV             0             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
  PCK1 MUTATED     2   2   1   0
  PCK1 WILD-TYPE 214  54 161   7
D20V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            2            214
  T2            2             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"
D20V5, binary
                cls
clus               0   1
  PCK1 MUTATED     3   0
  PCK1 WILD-TYPE 201  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      3    0
  PCK1 WILD-TYPE  201   16
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            3            201
  1            0             16
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus               0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 366  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      5    0
  PCK1 WILD-TYPE  366   70
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            5            366
  1            0             70
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  PCK1 MUTATED     2   3
  PCK1 WILD-TYPE 153 283
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    3
  PCK1 WILD-TYPE  153  283
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            2            153
  MALE              3            283
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             29 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5457 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-EU-5907 
"PCK1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED       0                         0     5
  PCK1 WILD-TYPE     7                        19   404
D20V9, multiclass
                           clus
vv                          PCK1 MUTATED PCK1 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                5            404
[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"
D20V10, binary
                cls
clus               0   1
  PCK1 MUTATED     0   3
  PCK1 WILD-TYPE  22 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    3
  PCK1 WILD-TYPE   22  286
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            3            286
[1] 2 2
[1] FALSE

Clustering(21) Variable = DPCR1 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 292 143
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             435 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              3             143 
$`DPCR1 MUTATED`
TCGA-B0-5080 TCGA-CW-5589 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 TCGA-DV-5576 
       11.24        78.18        61.41        47.01         1.94        23.90 

$`DPCR1 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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        11.64        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-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         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         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
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-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        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        77.36 
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        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         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-6093 
       85.78        66.31        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 
       58.75        14.66        60.59        63.39         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       56.94        55.33        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
       45.96        12.16        11.67        66.28        56.84        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           1.94            0.07 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          78.18          120.59 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         35.455          37.580 
[1] "1.9 - 78.2 (35.5)"  "0.1 - 120.6 (37.6)"
[1] "hr=" "1.7"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DPCR1 MUTATED         3        0         0        3
  DPCR1 WILD-TYPE     208       45       115       67
D21V3, multiclass
           clus
vv          DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I               3             208
  STAGE II              0              45
  STAGE III             0             115
  STAGE IV              3              67
[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 213  56 159   7
D21V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             3             213
  T2             0              56
  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"
D21V5, binary
                 cls
clus                0   1
  DPCR1 MUTATED     1   0
  DPCR1 WILD-TYPE 203  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      1    0
  DPCR1 WILD-TYPE  203   16
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             1             203
  1             0              16
[1] 2 2
[1] FALSE
D21V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 368  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      3    3
  DPCR1 WILD-TYPE  368   67
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             3             368
  1             3              67
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     2   4
  DPCR1 WILD-TYPE 153 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      2    4
  DPCR1 WILD-TYPE  153  282
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             2             153
  MALE               4             282
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              29 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5574      TCGA-DV-5575      TCGA-EU-5904      TCGA-EU-5905 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EU-5907 
"DPCR1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED       0                         1     5
  DPCR1 WILD-TYPE     7                        18   404
D21V9, multiclass
                           clus
vv                          DPCR1 MUTATED DPCR1 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              18
  WHITE                                 5             404
[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"
D21V10, binary
                 cls
clus                0   1
  DPCR1 MUTATED     0   6
  DPCR1 WILD-TYPE  22 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      0    6
  DPCR1 WILD-TYPE   22  283
                        clus
vv                       DPCR1 MUTATED DPCR1 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             6             283
[1] 2 2
[1] FALSE

Clustering(22) Variable = NFAT5 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  NFAT5 MUTATED     4   2
  NFAT5 WILD-TYPE 291 144
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             435 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              2             144 
$`NFAT5 MUTATED`
TCGA-AK-3431 TCGA-B0-4707 TCGA-B0-4718 TCGA-B0-5106 TCGA-B2-5633 TCGA-CW-6093 
       60.92        19.73        20.25        52.54        11.77       103.43 

$`NFAT5 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 
       84.36        73.08        66.31        15.78        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         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         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        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 
       11.64        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-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.87        90.48        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        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-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        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-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
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-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        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        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        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-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         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-4854 TCGA-CZ-4856 
        1.35        83.90        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
          11.77            0.07 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         103.43          120.59 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         36.395          37.580 
[1] "11.8 - 103.4 (36.4)" "0.1 - 120.6 (37.6)" 
[1] "hr=" "1.1"
D22V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NFAT5 MUTATED         3        1         2        0
  NFAT5 WILD-TYPE     208       44       113       70
D22V3, multiclass
           clus
vv          NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE I               3             208
  STAGE II              1              44
  STAGE III             2             113
  STAGE IV              0              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
  NFAT5 MUTATED     3   1   2   0
  NFAT5 WILD-TYPE 213  55 160   7
D22V4, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  T1             3             213
  T2             1              55
  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"
D22V5, binary
                 cls
clus                0   1
  NFAT5 MUTATED     2   0
  NFAT5 WILD-TYPE 202  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      2    0
  NFAT5 WILD-TYPE  202   16
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             2             202
  1             0              16
[1] 2 2
[1] FALSE
D22V6, binary
                 cls
clus                0   1
  NFAT5 MUTATED     6   0
  NFAT5 WILD-TYPE 365  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      6    0
  NFAT5 WILD-TYPE  365   70
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             6             365
  1             0              70
[1] 2 2
[1] FALSE
D22V7, binary
                 cls
clus                0   1
  NFAT5 MUTATED     1   5
  NFAT5 WILD-TYPE 154 281
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      1    5
  NFAT5 WILD-TYPE  154  281
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             1             154
  MALE               5             281
[1] 2 2
[1] FALSE
D22V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFAT5 MUTATED       0                         0     6
  NFAT5 WILD-TYPE     7                        19   403
D22V9, multiclass
                           clus
vv                          NFAT5 MUTATED NFAT5 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              19
  WHITE                                 6             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"
D22V10, binary
                 cls
clus                0   1
  NFAT5 MUTATED     0   6
  NFAT5 WILD-TYPE  22 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0    6
  NFAT5 WILD-TYPE   22  283
                        clus
vv                       NFAT5 MUTATED NFAT5 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             6             283
[1] 2 2
[1] FALSE

Clustering(23) Variable = EGFR MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     2   5
  EGFR WILD-TYPE 293 141
  EGFR MUTATED EGFR WILD-TYPE 
             7            434 
  EGFR MUTATED EGFR WILD-TYPE 
             5            141 
$`EGFR MUTATED`
TCGA-B0-4822 TCGA-B0-4849 TCGA-B0-5116 TCGA-B0-5713 TCGA-BP-4341 TCGA-BP-4354 
       36.53         2.27        21.60        61.32        52.24        33.99 
TCGA-CJ-4868 
       21.24 

$`EGFR WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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-B0-5117 
       29.95        19.30        35.90        11.80        26.20        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
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        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4343 
       80.68         0.07        93.99        18.48        74.17        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-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         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         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
       75.88        65.69        54.61        58.95        11.05        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        77.36 
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        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        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        63.88        72.00        79.89        84.66 
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        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 
        6.77         4.18 

  EGFR MUTATED EGFR WILD-TYPE 
          2.27           0.07 
  EGFR MUTATED EGFR WILD-TYPE 
         61.32         120.59 
  EGFR MUTATED EGFR WILD-TYPE 
         33.99          38.35 
[1] "2.3 - 61.3 (34.0)"  "0.1 - 120.6 (38.3)"
[1] "hr=" "2.8"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EGFR MUTATED         0        1         4        2
  EGFR WILD-TYPE     211       44       111       68
D23V3, multiclass
           clus
vv          EGFR MUTATED EGFR WILD-TYPE
  STAGE I              0            211
  STAGE II             1             44
  STAGE III            4            111
  STAGE IV             2             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
  EGFR MUTATED     0   1   5   1
  EGFR WILD-TYPE 216  55 157   6
D23V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            0            216
  T2            1             55
  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"
D23V5, binary
                cls
clus               0   1
  EGFR MUTATED     3   1
  EGFR WILD-TYPE 201  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      3    1
  EGFR WILD-TYPE  201   15
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            3            201
  1            1             15
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus               0   1
  EGFR MUTATED     5   2
  EGFR WILD-TYPE 366  68
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      5    2
  EGFR WILD-TYPE  366   68
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            5            366
  1            2             68
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  EGFR MUTATED     1   6
  EGFR WILD-TYPE 154 280
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      1    6
  EGFR WILD-TYPE  154  280
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            1            154
  MALE              6            280
[1] 2 2
[1] FALSE
D23V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED       0                         0     7
  EGFR WILD-TYPE     7                        19   402
D23V9, multiclass
                           clus
vv                          EGFR MUTATED EGFR WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                7            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"
D23V10, binary
                cls
clus               0   1
  EGFR MUTATED     0   5
  EGFR WILD-TYPE  22 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0    5
  EGFR WILD-TYPE   22  284
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            5            284
[1] 2 2
[1] FALSE

Clustering(24) Variable = TRIM6 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  TRIM6 MUTATED     2   3
  TRIM6 WILD-TYPE 293 143
  TRIM6 MUTATED TRIM6 WILD-TYPE 
              5             436 
  TRIM6 MUTATED TRIM6 WILD-TYPE 
              3             143 
$`TRIM6 MUTATED`
TCGA-B0-4713 TCGA-B0-5083 TCGA-B4-5844 TCGA-BP-4988 TCGA-CZ-5986 
        6.64        34.36         0.23        27.22        12.26 

$`TRIM6 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       19.73         3.16        43.96         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
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-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       67.96        65.65        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  TRIM6 MUTATED TRIM6 WILD-TYPE 
           0.23            0.07 
  TRIM6 MUTATED TRIM6 WILD-TYPE 
          34.36          120.59 
  TRIM6 MUTATED TRIM6 WILD-TYPE 
          12.26           38.48 
[1] "0.2 - 34.4 (12.3)"  "0.1 - 120.6 (38.5)"
[1] "hr=" "4.8"
D24V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TRIM6 MUTATED         3        1         1        0
  TRIM6 WILD-TYPE     208       44       114       70
D24V3, multiclass
           clus
vv          TRIM6 MUTATED TRIM6 WILD-TYPE
  STAGE I               3             208
  STAGE II              1              44
  STAGE III             1             114
  STAGE IV              0              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
  TRIM6 MUTATED     3   1   1   0
  TRIM6 WILD-TYPE 213  55 161   7
D24V4, multiclass
    clus
vv   TRIM6 MUTATED TRIM6 WILD-TYPE
  T1             3             213
  T2             1              55
  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"
D24V5, binary
                 cls
clus                0   1
  TRIM6 MUTATED     4   0
  TRIM6 WILD-TYPE 200  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM6 MUTATED      4    0
  TRIM6 WILD-TYPE  200   16
   clus
vv  TRIM6 MUTATED TRIM6 WILD-TYPE
  0             4             200
  1             0              16
[1] 2 2
[1] FALSE
D24V6, binary
                 cls
clus                0   1
  TRIM6 MUTATED     5   0
  TRIM6 WILD-TYPE 366  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM6 MUTATED      5    0
  TRIM6 WILD-TYPE  366   70
   clus
vv  TRIM6 MUTATED TRIM6 WILD-TYPE
  0             5             366
  1             0              70
[1] 2 2
[1] FALSE
D24V7, binary
                 cls
clus                0   1
  TRIM6 MUTATED     2   3
  TRIM6 WILD-TYPE 153 283
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM6 MUTATED      2    3
  TRIM6 WILD-TYPE  153  283
        clus
vv       TRIM6 MUTATED TRIM6 WILD-TYPE
  FEMALE             2             153
  MALE               3             283
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "TRIM6 MUTATED"         
clus
  TRIM6 MUTATED TRIM6 WILD-TYPE 
              1              29 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-B4-5843      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905 
"TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" "TRIM6 WILD-TYPE" 
     TCGA-EU-5907 
"TRIM6 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIM6 MUTATED       0                         0     5
  TRIM6 WILD-TYPE     7                        19   404
D24V9, multiclass
                           clus
vv                          TRIM6 MUTATED TRIM6 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              19
  WHITE                                 5             404
[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"
D24V10, binary
                 cls
clus                0   1
  TRIM6 MUTATED     0   3
  TRIM6 WILD-TYPE  22 286
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TRIM6 MUTATED      0    3
  TRIM6 WILD-TYPE   22  286
                        clus
vv                       TRIM6 MUTATED TRIM6 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             3             286
[1] 2 2
[1] FALSE

Clustering(25) Variable = RBMX MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  RBMX MUTATED     3   1
  RBMX WILD-TYPE 292 145
  RBMX MUTATED RBMX WILD-TYPE 
             4            437 
  RBMX MUTATED RBMX WILD-TYPE 
             1            145 
$`RBMX MUTATED`
TCGA-AS-3778 TCGA-B0-4712 TCGA-B8-5158 TCGA-CZ-5988 
        1.41        43.96        20.91        22.78 

$`RBMX WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       28.04        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-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        3.16         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         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        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        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 
       63.88        72.00        79.89        84.66        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        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
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-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        14.63        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  RBMX MUTATED RBMX WILD-TYPE 
          1.41           0.07 
  RBMX MUTATED RBMX WILD-TYPE 
         43.96         120.59 
  RBMX MUTATED RBMX WILD-TYPE 
        21.845         38.300 
[1] "1.4 - 44.0 (21.8)"  "0.1 - 120.6 (38.3)"
[1] "hr=" "1.5"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RBMX MUTATED         2        0         1        1
  RBMX WILD-TYPE     209       45       114       69
D25V3, multiclass
           clus
vv          RBMX MUTATED RBMX WILD-TYPE
  STAGE I              2            209
  STAGE II             0             45
  STAGE III            1            114
  STAGE IV             1             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
  RBMX MUTATED     2   0   2   0
  RBMX WILD-TYPE 214  56 160   7
D25V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            2            214
  T2            0             56
  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"
D25V5, binary
                cls
clus               0   1
  RBMX MUTATED     1   1
  RBMX WILD-TYPE 203  15
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      1    1
  RBMX WILD-TYPE  203   15
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            1            203
  1            1             15
[1] 2 2
[1] FALSE
D25V6, binary
                cls
clus               0   1
  RBMX MUTATED     3   1
  RBMX WILD-TYPE 368  69
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      3    1
  RBMX WILD-TYPE  368   69
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            3            368
  1            1             69
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus               0   1
  RBMX MUTATED     0   4
  RBMX WILD-TYPE 155 282
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    4
  RBMX WILD-TYPE  155  282
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            0            155
  MALE              4            282
[1] 2 2
[1] FALSE
D25V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED       0                         0     4
  RBMX WILD-TYPE     7                        19   405
D25V9, multiclass
                           clus
vv                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                4            405
[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"
D25V10, binary
                cls
clus               0   1
  RBMX MUTATED     0   3
  RBMX WILD-TYPE  22 286
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    3
  RBMX WILD-TYPE   22  286
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            3            286
[1] 2 2
[1] FALSE

Clustering(26) Variable = GPR172B MUTATION ANALYSIS
D26V1, survival
                   sevent
clus2                 0   1
  GPR172B MUTATED     3   1
  GPR172B WILD-TYPE 292 145
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               437 
  GPR172B MUTATED GPR172B WILD-TYPE 
                1               145 
$`GPR172B MUTATED`
TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4761 TCGA-BP-4782 
       99.85        77.03         5.98        11.64 

$`GPR172B WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         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-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        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        11.64        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-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        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        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         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 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.53        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        32.61         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       23.05        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        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-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       56.91        68.38        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  GPR172B MUTATED GPR172B WILD-TYPE 
             5.98              0.07 
  GPR172B MUTATED GPR172B WILD-TYPE 
            99.85            120.59 
  GPR172B MUTATED GPR172B WILD-TYPE 
           44.335            37.580 
[1] "6.0 - 99.8 (44.3)"  "0.1 - 120.6 (37.6)"
[1] "hr=" "1.7"
D26V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  GPR172B MUTATED         3        0         1        0
  GPR172B WILD-TYPE     208       45       114       70
D26V3, multiclass
           clus
vv          GPR172B MUTATED GPR172B WILD-TYPE
  STAGE I                 3               208
  STAGE II                0                45
  STAGE III               1               114
  STAGE IV                0                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
  GPR172B MUTATED     3   0   1   0
  GPR172B WILD-TYPE 213  56 161   7
D26V4, multiclass
    clus
vv   GPR172B MUTATED GPR172B WILD-TYPE
  T1               3               213
  T2               0                56
  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"
D26V5, binary
                   cls
clus                  0   1
  GPR172B MUTATED     2   1
  GPR172B WILD-TYPE 202  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      2    1
  GPR172B WILD-TYPE  202   15
   clus
vv  GPR172B MUTATED GPR172B WILD-TYPE
  0               2               202
  1               1                15
[1] 2 2
[1] FALSE
D26V6, binary
                   cls
clus                  0   1
  GPR172B MUTATED     4   0
  GPR172B WILD-TYPE 367  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      4    0
  GPR172B WILD-TYPE  367   70
   clus
vv  GPR172B MUTATED GPR172B WILD-TYPE
  0               4               367
  1               0                70
[1] 2 2
[1] FALSE
D26V7, binary
                   cls
clus                  0   1
  GPR172B MUTATED     3   1
  GPR172B WILD-TYPE 152 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      3    1
  GPR172B WILD-TYPE  152  285
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  FEMALE               3               152
  MALE                 1               285
[1] 2 2
[1] FALSE
D26V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR172B MUTATED       0                         0     4
  GPR172B WILD-TYPE     7                        19   405
D26V9, multiclass
                           clus
vv                          GPR172B MUTATED GPR172B WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                19
  WHITE                                   4               405
[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"
D26V10, binary
                   cls
clus                  0   1
  GPR172B MUTATED     1   0
  GPR172B WILD-TYPE  21 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      1    0
  GPR172B WILD-TYPE   21  289
                        clus
vv                       GPR172B MUTATED GPR172B WILD-TYPE
  HISPANIC OR LATINO                   1                21
  NOT HISPANIC OR LATINO               0               289
[1] 2 2
[1] FALSE

Clustering(27) Variable = FGFR3 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED     3   1
  FGFR3 WILD-TYPE 292 145
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             437 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              1             145 
$`FGFR3 MUTATED`
TCGA-AK-3445 TCGA-B0-5109 TCGA-B2-4101 TCGA-CJ-4908 
       42.08        19.30        21.30        50.33 

$`FGFR3 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       67.20        57.37        46.78        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
        1.68        12.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         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        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        49.28        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
          19.30            0.07 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          50.33          120.59 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          31.69           37.58 
[1] "19.3 - 50.3 (31.7)" "0.1 - 120.6 (37.6)"
[1] "hr=" "1"  
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FGFR3 MUTATED         1        1         2        0
  FGFR3 WILD-TYPE     210       44       113       70
D27V3, multiclass
           clus
vv          FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I               1             210
  STAGE II              1              44
  STAGE III             2             113
  STAGE IV              0              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
  FGFR3 MUTATED     1   1   2   0
  FGFR3 WILD-TYPE 215  55 160   7
D27V4, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  T1             1             215
  T2             1              55
  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"
D27V5, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   1
  FGFR3 WILD-TYPE 204  15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    1
  FGFR3 WILD-TYPE  204   15
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0             0             204
  1             1              15
[1] 2 2
[1] FALSE
D27V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED     4   0
  FGFR3 WILD-TYPE 367  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      4    0
  FGFR3 WILD-TYPE  367   70
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0             4             367
  1             0              70
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   4
  FGFR3 WILD-TYPE 155 282
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    4
  FGFR3 WILD-TYPE  155  282
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             0             155
  MALE               4             282
[1] 2 2
[1] FALSE
D27V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED       0                         0     4
  FGFR3 WILD-TYPE     7                        19   405
D27V9, multiclass
                           clus
vv                          FGFR3 MUTATED FGFR3 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              19
  WHITE                                 4             405
[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"
D27V10, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   4
  FGFR3 WILD-TYPE  22 285
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    4
  FGFR3 WILD-TYPE   22  285
                        clus
vv                       FGFR3 MUTATED FGFR3 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             4             285
[1] 2 2
[1] FALSE

Clustering(28) Variable = ARAP3 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 293 145
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             438 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             145 
$`ARAP3 MUTATED`
TCGA-A3-3323 TCGA-B0-4819 TCGA-CJ-4870 
       36.36         6.02        49.25 

$`ARAP3 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.08        49.02        48.59        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
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 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         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        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        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 
       63.88        72.00        79.89        84.66        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        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
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-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           6.02            0.07 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          49.25          120.59 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          36.36           37.94 
[1] "6.0 - 49.2 (36.4)"  "0.1 - 120.6 (37.9)"
[1] "hr=" "1.4"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ARAP3 MUTATED         1        0         1        1
  ARAP3 WILD-TYPE     210       45       114       69
D28V3, multiclass
           clus
vv          ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I               1             210
  STAGE II              0              45
  STAGE III             1             114
  STAGE IV              1              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
  ARAP3 MUTATED     1   0   2   0
  ARAP3 WILD-TYPE 215  56 160   7
D28V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1             215
  T2             0              56
  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"
D28V5, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   0
  ARAP3 WILD-TYPE 204  16
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    0
  ARAP3 WILD-TYPE  204   16
D28V6, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 369  69
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  369   69
   clus
vv  ARAP3 MUTATED ARAP3 WILD-TYPE
  0             2             369
  1             1              69
[1] 2 2
[1] FALSE
D28V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 153 285
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  153  285
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE             2             153
  MALE               1             285
[1] 2 2
[1] FALSE
D28V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED       0                         1     2
  ARAP3 WILD-TYPE     7                        18   407
D28V9, multiclass
                           clus
vv                          ARAP3 MUTATED ARAP3 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              18
  WHITE                                 2             407
[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"
D28V10, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   2
  ARAP3 WILD-TYPE  22 287
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    2
  ARAP3 WILD-TYPE   22  287
                        clus
vv                       ARAP3 MUTATED ARAP3 WILD-TYPE
  HISPANIC OR LATINO                 0              22
  NOT HISPANIC OR LATINO             2             287
[1] 2 2
[1] FALSE

Clustering(29) Variable = OPTC MUTATION ANALYSIS
D29V1, survival
                sevent
clus2              0   1
  OPTC MUTATED     3   1
  OPTC WILD-TYPE 292 145
  OPTC MUTATED OPTC WILD-TYPE 
             4            437 
  OPTC MUTATED OPTC WILD-TYPE 
             1            145 
$`OPTC MUTATED`
TCGA-A3-3311 TCGA-BP-4782 TCGA-BP-4795 TCGA-CJ-4901 
       39.16        11.64        20.38        47.67 

$`OPTC WILD-TYPE`
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        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-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
       61.97        60.59        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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        77.36        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        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
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-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  OPTC MUTATED OPTC WILD-TYPE 
         11.64           0.07 
  OPTC MUTATED OPTC WILD-TYPE 
         47.67         120.59 
  OPTC MUTATED OPTC WILD-TYPE 
         29.77          37.58 
[1] "11.6 - 47.7 (29.8)" "0.1 - 120.6 (37.6)"
[1] "hr=" "1.1"
D29V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  OPTC MUTATED         3        0         1        0
  OPTC WILD-TYPE     208       45       114       70
D29V3, multiclass
           clus
vv          OPTC MUTATED OPTC WILD-TYPE
  STAGE I              3            208
  STAGE II             0             45
  STAGE III            1            114
  STAGE IV             0             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
  OPTC MUTATED     3   0   1   0
  OPTC WILD-TYPE 213  56 161   7
D29V4, multiclass
    clus
vv   OPTC MUTATED OPTC WILD-TYPE
  T1            3            213
  T2            0             56
  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"
D29V5, binary
                cls
clus               0   1
  OPTC MUTATED     1   0
  OPTC WILD-TYPE 203  16
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTC MUTATED      1    0
  OPTC WILD-TYPE  203   16
   clus
vv  OPTC MUTATED OPTC WILD-TYPE
  0            1            203
  1            0             16
[1] 2 2
[1] FALSE
D29V6, binary
                cls
clus               0   1
  OPTC MUTATED     4   0
  OPTC WILD-TYPE 367  70
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTC MUTATED      4    0
  OPTC WILD-TYPE  367   70
   clus
vv  OPTC MUTATED OPTC WILD-TYPE
  0            4            367
  1            0             70
[1] 2 2
[1] FALSE
D29V7, binary
                cls
clus               0   1
  OPTC MUTATED     2   2
  OPTC WILD-TYPE 153 284
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTC MUTATED      2    2
  OPTC WILD-TYPE  153  284
        clus
vv       OPTC MUTATED OPTC WILD-TYPE
  FEMALE            2            153
  MALE              2            284
[1] 2 2
[1] FALSE
D29V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  OPTC MUTATED       0                         0     3
  OPTC WILD-TYPE     7                        19   406
D29V9, multiclass
                           clus
vv                          OPTC MUTATED OPTC WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             19
  WHITE                                3            406
[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"
D29V10, binary
                cls
clus               0   1
  OPTC MUTATED     0   1
  OPTC WILD-TYPE  22 288
[1] "tbl2"
                cls
clus             [,1] [,2]
  OPTC MUTATED      0    1
  OPTC WILD-TYPE   22  288
                        clus
vv                       OPTC MUTATED OPTC WILD-TYPE
  HISPANIC OR LATINO                0             22
  NOT HISPANIC OR LATINO            1            288
[1] 2 2
[1] FALSE

Clustering(30) Variable = GOLGA5 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2                0   1
  GOLGA5 MUTATED     4   1
  GOLGA5 WILD-TYPE 291 145
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
               5              436 
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
               1              145 
$`GOLGA5 MUTATED`
TCGA-A3-3323 TCGA-BP-4165 TCGA-BP-5199 TCGA-CJ-4884 TCGA-CZ-4861 
       36.36        99.85        44.55        57.83        14.66 

$`GOLGA5 WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.08        49.02        48.59        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        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        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         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        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61         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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        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-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        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-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        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        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        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        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
       46.16         0.59        47.08        69.21        58.75        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        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-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
           14.66             0.07 
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
           99.85           120.59 
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
           44.55            37.53 
[1] "14.7 - 99.8 (44.5)" "0.1 - 120.6 (37.5)"
[1] "hr=" "2.1"
D30V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GOLGA5 MUTATED         2        2         1        0
  GOLGA5 WILD-TYPE     209       43       114       70
D30V3, multiclass
           clus
vv          GOLGA5 MUTATED GOLGA5 WILD-TYPE
  STAGE I                2              209
  STAGE II               2               43
  STAGE III              1              114
  STAGE IV               0               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
  GOLGA5 MUTATED     2   2   1   0
  GOLGA5 WILD-TYPE 214  54 161   7
D30V4, multiclass
    clus
vv   GOLGA5 MUTATED GOLGA5 WILD-TYPE
  T1              2              214
  T2              2               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"
D30V5, binary
                  cls
clus                 0   1
  GOLGA5 MUTATED     2   0
  GOLGA5 WILD-TYPE 202  16
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA5 MUTATED      2    0
  GOLGA5 WILD-TYPE  202   16
   clus
vv  GOLGA5 MUTATED GOLGA5 WILD-TYPE
  0              2              202
  1              0               16
[1] 2 2
[1] FALSE
D30V6, binary
                  cls
clus                 0   1
  GOLGA5 MUTATED     5   0
  GOLGA5 WILD-TYPE 366  70
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA5 MUTATED      5    0
  GOLGA5 WILD-TYPE  366   70
   clus
vv  GOLGA5 MUTATED GOLGA5 WILD-TYPE
  0              5              366
  1              0               70
[1] 2 2
[1] FALSE
D30V7, binary
                  cls
clus                 0   1
  GOLGA5 MUTATED     2   3
  GOLGA5 WILD-TYPE 153 283
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA5 MUTATED      2    3
  GOLGA5 WILD-TYPE  153  283
        clus
vv       GOLGA5 MUTATED GOLGA5 WILD-TYPE
  FEMALE              2              153
  MALE                3              283
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "GOLGA5 MUTATED"        
clus
  GOLGA5 MUTATED GOLGA5 WILD-TYPE 
               1               29 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905 
"GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" "GOLGA5 WILD-TYPE" 
      TCGA-EU-5907 
"GOLGA5 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GOLGA5 MUTATED       0                         0     5
  GOLGA5 WILD-TYPE     7                        19   404
D30V9, multiclass
                           clus
vv                          GOLGA5 MUTATED GOLGA5 WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              0               19
  WHITE                                  5              404
[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"
D30V10, binary
                  cls
clus                 0   1
  GOLGA5 MUTATED     0   2
  GOLGA5 WILD-TYPE  22 287
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GOLGA5 MUTATED      0    2
  GOLGA5 WILD-TYPE   22  287
                        clus
vv                       GOLGA5 MUTATED GOLGA5 WILD-TYPE
  HISPANIC OR LATINO                  0               22
  NOT HISPANIC OR LATINO              2              287
[1] 2 2
[1] FALSE
