[1] "ofn"         "-oTKIPAN-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/KIPAN-TP/19775252/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/20230417/transformed.cor.cli.txt"

nPatients in clinical file=938, in cluster file=703, common to both=663
[1]  57 663
[1] "FAM18B2 MUTATION ANALYSIS"
[1] 3
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               35               628 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               35               628 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            35            628 
  TP53 MUTATED TP53 WILD-TYPE 
            35            628 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            26            637 
  PTEN MUTATED PTEN WILD-TYPE 
            26            637 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             28             635 
  KDM5C MUTATED KDM5C WILD-TYPE 
             28             635 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             56             607 
  SETD2 MUTATED SETD2 WILD-TYPE 
             56             607 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            138             525 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            138             525 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            16            647 
  NEFH MUTATED NEFH WILD-TYPE 
            16            647 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          195           468 
  VHL MUTATED VHL WILD-TYPE 
          195           468 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           19           644 
  MET MUTATED MET WILD-TYPE 
           19           644 
[1] "HNRNPM MUTATION ANALYSIS"
[1] 3
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              651 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              651 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           16           647 
  NF2 MUTATED NF2 WILD-TYPE 
           16           647 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            5           658 
  TDG MUTATED TDG WILD-TYPE 
            5           658 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             32             631 
  MUC5B MUTATED MUC5B WILD-TYPE 
             32             631 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              650 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              650 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   8                  655 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   8                  655 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             658 
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             658 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             649 
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             649 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              653 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              653 
[1] "KDELR3 MUTATION ANALYSIS"
[1] 3
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               6              657 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               6              657 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           16           647 
  ATM MUTATED ATM WILD-TYPE 
           16           647 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            32            631 
  MTOR MUTATED MTOR WILD-TYPE 
            32            631 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             6            657 
  EGFR MUTATED EGFR WILD-TYPE 
             6            657 
[1] "SLC6A14 MUTATION ANALYSIS"
[1] 3
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               658 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               658 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              651 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              651 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            659 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            659 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              658 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              658 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
             7            656 
  RAI1 MUTATED RAI1 WILD-TYPE 
             7            656 
[1] "FAM160B2 MUTATION ANALYSIS"
[1] 3
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                659 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                659 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              11              652 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              11              652 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             653 
  KDM6A MUTATED KDM6A WILD-TYPE 
             10             653 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             655 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             655 
[1] "CYP4F11 MUTATION ANALYSIS"
[1] 3
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               658 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               658 
[1] "STAM MUTATION ANALYSIS"
[1] 3
  STAM MUTATED STAM WILD-TYPE 
             6            657 
  STAM MUTATED STAM WILD-TYPE 
             6            657 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              658 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              658 
[1] "PARD6B MUTATION ANALYSIS"
[1] 3
  PARD6B MUTATED PARD6B WILD-TYPE 
               5              658 
  PARD6B MUTATED PARD6B WILD-TYPE 
               5              658 
[1] "RHEB MUTATION ANALYSIS"
[1] 3
  RHEB MUTATED RHEB WILD-TYPE 
             3            660 
  RHEB MUTATED RHEB WILD-TYPE 
             3            660 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               660 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               660 
[1] "SKI MUTATION ANALYSIS"
[1] 3
  SKI MUTATED SKI WILD-TYPE 
            9           654 
  SKI MUTATED SKI WILD-TYPE 
            9           654 
[1] "THBS1 MUTATION ANALYSIS"
[1] 3
  THBS1 MUTATED THBS1 WILD-TYPE 
             10             653 
  THBS1 MUTATED THBS1 WILD-TYPE 
             10             653 
[1] "SH3BP2 MUTATION ANALYSIS"
[1] 3
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              659 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              659 
[1] "NASP MUTATION ANALYSIS"
[1] 3
  NASP MUTATED NASP WILD-TYPE 
             4            659 
  NASP MUTATED NASP WILD-TYPE 
             4            659 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            21            642 
  FAT1 MUTATED FAT1 WILD-TYPE 
            21            642 
[1] "CACNA1C MUTATION ANALYSIS"
[1] 3
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               17               646 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               17               646 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            658 
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            658 
[1] "TPPP MUTATION ANALYSIS"
[1] 3
  TPPP MUTATED TPPP WILD-TYPE 
             3            660 
  TPPP MUTATED TPPP WILD-TYPE 
             3            660 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            38            625 
  MLL3 MUTATED MLL3 WILD-TYPE 
            38            625 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            4           659 
  PAM MUTATED PAM WILD-TYPE 
            4           659 
[1] "GAPDHS MUTATION ANALYSIS"
[1] 3
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              658 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              658 
[1] "TMCO3 MUTATION ANALYSIS"
[1] 3
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             656 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             656 
[1] "RPL7A MUTATION ANALYSIS"
[1] 3
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             660 
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             660 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                656 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                656 
[1] "AHNAK2 MUTATION ANALYSIS"
[1] 3
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              630 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              630 
[1] "JMJD1C MUTATION ANALYSIS"
[1] 3
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              10              653 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              10              653 
[1] "TTLL6 MUTATION ANALYSIS"
[1] 3
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              6             657 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              6             657 
[1] "AMAC1L3 MUTATION ANALYSIS"
[1] 3
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                8               655 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                8               655 
[1] "TRAPPC9 MUTATION ANALYSIS"
[1] 3
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                5               658 
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                5               658 
[1] "MED16 MUTATION ANALYSIS"
[1] 3
  MED16 MUTATED MED16 WILD-TYPE 
              4             659 
  MED16 MUTATED MED16 WILD-TYPE 
              4             659 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 663 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=62,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=172,	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=464,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "246"   "1"    
freq.contrast "1"     "246"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 663 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=62, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
337  95 221  10 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
337  95 221  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
337  95 221  10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
337  95 221  10 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
272  35   6 
[1] "table(vv)"
vv
 N0  N1  N2 
272  35   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
272  35   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
272  35   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=28, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=24, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = FAM18B2 MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  FAM18B2 MUTATED    29   5
  FAM18B2 WILD-TYPE 447 178
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
               34               625 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                5               178 
$`FAM18B2 MUTATED`
TCGA-A4-7828 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-A5XZ TCGA-B3-3925 TCGA-B9-4113 
        7.82        25.64        23.31        15.75        33.83        50.50 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5882 
       28.18         0.46        43.99         0.16        63.72        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       40.83        26.04         0.95         7.92         2.76       123.62 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-7837 TCGA-DW-7839 TCGA-DZ-6131 
       50.40         7.63         7.17        37.55        13.78        79.86 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.19        61.02        74.60        24.89         4.01        51.78 
TCGA-G7-6797 TCGA-GL-A4EM TCGA-MH-A55W TCGA-P4-A5EB 
       25.15         1.05        34.29        99.12 

$`FAM18B2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.10        21.37        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 
       16.64        30.48        29.46        23.97        23.28        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        21.07        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-7268 TCGA-B9-A44B 
       34.49        12.46        26.40        20.61        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       19.23        17.23        14.86        86.76        19.27         8.88 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       22.92        43.20        47.80        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-7045 TCGA-BQ-7046 
       13.25        10.82         7.66        11.97        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 
       93.34        61.28        49.84        26.27        11.28         7.04 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7838 TCGA-DW-7840 
        3.81        48.85        13.61       129.86        24.46         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-EV-5901 TCGA-EV-5902 
       14.63         3.02        40.77        80.88        34.19        19.00 
TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       10.68        90.90        11.05        39.25        71.44        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       29.10        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       87.09        42.94         6.61        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
             0.16              0.07 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
           123.62            194.79 
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
            25.84             38.30 
[1] "0.2 - 123.6 (25.8)" "0.1 - 194.8 (38.3)"
[1] "hr=" "1.5"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM18B2 MUTATED        19        2         8        3
  FAM18B2 WILD-TYPE     306       74       155       85
D1V3, multiclass
           clus
vv          FAM18B2 MUTATED FAM18B2 WILD-TYPE
  STAGE I                19               306
  STAGE II                2                74
  STAGE III               8               155
  STAGE IV                3                85
[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
  FAM18B2 MUTATED    20   5  10   0
  FAM18B2 WILD-TYPE 317  90 211  10
D1V4, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  T1              20               317
  T2               5                90
  T3              10               211
  T4               0                10
[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                 N0  N1  N2
  FAM18B2 MUTATED     4   3   1
  FAM18B2 WILD-TYPE 268  32   5
D1V5, multiclass
    clus
vv   FAM18B2 MUTATED FAM18B2 WILD-TYPE
  N0               4               268
  N1               3                32
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  FAM18B2 MUTATED    13   2
  FAM18B2 WILD-TYPE 450  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     13    2
  FAM18B2 WILD-TYPE  450   76
   clus
vv  FAM18B2 MUTATED FAM18B2 WILD-TYPE
  0              13               450
  1               2                76
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  FAM18B2 MUTATED    11  24
  FAM18B2 WILD-TYPE 218 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED     11   24
  FAM18B2 WILD-TYPE  218  410
        clus
vv       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  FEMALE              11               218
  MALE                24               410
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM18B2 MUTATED                    0                                 0
  FAM18B2 WILD-TYPE                 66                               436
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM18B2 MUTATED                                      35
  FAM18B2 WILD-TYPE                                   126
D1V9, multiclass
                                       clus
vv                                      FAM18B2 MUTATED FAM18B2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   0               436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              35               126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
[1] "Remove cluster labels:" "FAM18B2 MUTATED"       
clus
  FAM18B2 MUTATED FAM18B2 WILD-TYPE 
                2                30 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3451        TCGA-B8-5158        TCGA-B8-5550 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-A69E        TCGA-DW-5561 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-DW-7963        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-GL-7773        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-P4-A5E6 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"FAM18B2 WILD-TYPE" "FAM18B2 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM18B2 MUTATED                                  1     0
  FAM18B2 WILD-TYPE                                1    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM18B2 MUTATED                           8    22
  FAM18B2 WILD-TYPE                        58   543
D1V12, multiclass
                                  clus
vv                                 FAM18B2 MUTATED FAM18B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      8                58
  WHITE                                         22               543
[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"
D1V13, binary
                   cls
clus                  0   1
  FAM18B2 MUTATED     1  23
  FAM18B2 WILD-TYPE  30 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM18B2 MUTATED      1   23
  FAM18B2 WILD-TYPE   30  418
                        clus
vv                       FAM18B2 MUTATED FAM18B2 WILD-TYPE
  HISPANIC OR LATINO                   1                30
  NOT HISPANIC OR LATINO              23               418
[1] 2 2
[1] FALSE

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    24  11
  TP53 WILD-TYPE 452 172
  TP53 MUTATED TP53 WILD-TYPE 
            35            624 
  TP53 MUTATED TP53 WILD-TYPE 
            11            172 
$`TP53 MUTATED`
TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
      141.73        90.48        92.55        30.25        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8341 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8428 
       28.11        24.79       129.37        25.91        65.19        52.27 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 
       19.33        11.21        59.08        42.35       105.47        10.68 
TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-AK-3440 TCGA-B0-4710 
       16.67        99.88       105.60        90.48        94.19        57.70 
TCGA-B0-5098 TCGA-B0-5117 TCGA-BP-4176 TCGA-BP-4770 TCGA-CJ-5677 TCGA-CZ-4865 
       52.08        52.87        64.27        10.82        25.71         5.46 
TCGA-CZ-5463 TCGA-A4-A57E TCGA-B1-A655 TCGA-B3-4104 TCGA-BQ-5881 
       21.76         8.48        16.77        34.49        47.80 

$`TP53 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
       38.07        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 
       98.96        84.89        98.33        96.95        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8426 
       31.33        23.47        87.91        25.48       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8405 
        0.99        87.12         2.50       115.00       100.87       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 
      103.40        92.71       104.55       103.10       130.13        96.62 
TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       92.55        39.16        24.16        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 
       37.38        48.82        52.93        45.53        88.37        42.97 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 
       15.78        73.68        68.61       109.51        46.78        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       38.40        82.45        72.89        12.13        40.70         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-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        2.14        19.73        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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-4177 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        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-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       48.07        13.15         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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       129.40       133.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        61.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        24.56        20.25        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  TP53 MUTATED TP53 WILD-TYPE 
          5.46           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        141.73         194.79 
  TP53 MUTATED TP53 WILD-TYPE 
        47.800         37.235 
[1] "5.5 - 141.7 (47.8)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1"  
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED        12       10         6        7
  TP53 WILD-TYPE     313       66       157       81
D2V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             12            313
  STAGE II            10             66
  STAGE III            6            157
  STAGE IV             7             81
[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    12  11  10   2
  TP53 WILD-TYPE 325  84 211   8
D2V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           12            325
  T2           11             84
  T3           10            211
  T4            2              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TP53 MUTATED    15   2   2
  TP53 WILD-TYPE 257  33   4
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           15            257
  N1            2             33
  N2            2              4
[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"
D2V6, binary
                cls
clus               0   1
  TP53 MUTATED    21   3
  TP53 WILD-TYPE 442  75
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     21    3
  TP53 WILD-TYPE  442   75
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           21            442
  1            3             75
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  TP53 MUTATED    15  20
  TP53 WILD-TYPE 214 414
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     15   20
  TP53 WILD-TYPE  214  414
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           15            214
  MALE             20            414
[1] 2 2
[1] FALSE
D2V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TP53 MUTATED                   22                                 9
  TP53 WILD-TYPE                 44                               427
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TP53 MUTATED                                       4
  TP53 WILD-TYPE                                   157
D2V9, multiclass
                                       clus
vv                                      TP53 MUTATED TP53 WILD-TYPE
  KIDNEY CHROMOPHOBE                              22             44
  KIDNEY CLEAR CELL RENAL CARCINOMA                9            427
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            4            157
[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, continuous
D2V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     2
  TP53 WILD-TYPE                                2     8
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           2    30
  TP53 WILD-TYPE                        64   535
D2V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2              8
  BLACK OR AFRICAN AMERICAN                   2             64
  WHITE                                      30            535
[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"
D2V13, binary
                cls
clus               0   1
  TP53 MUTATED     1  20
  TP53 WILD-TYPE  30 421
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   20
  TP53 WILD-TYPE   30  421
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO           20            421
[1] 2 2
[1] FALSE

Clustering(3) Variable = PTEN MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    18   8
  PTEN WILD-TYPE 458 175
  PTEN MUTATED PTEN WILD-TYPE 
            26            633 
  PTEN MUTATED PTEN WILD-TYPE 
             8            175 
$`PTEN MUTATED`
TCGA-KL-8323 TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 
       38.07        90.48        30.25        54.74        16.67        96.62 
TCGA-AK-3427 TCGA-B0-4694 TCGA-B0-4810 TCGA-B0-4843 TCGA-B8-4621 TCGA-B8-5158 
      117.80         3.48        15.72        10.52        25.91        20.91 
TCGA-BP-4161 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4351 TCGA-BP-5010 TCGA-BP-5199 
       90.28        53.42        49.84        31.89        28.87        44.55 
TCGA-CJ-4871 TCGA-DV-5568 TCGA-EU-5907 TCGA-A4-7996 TCGA-B1-A657 TCGA-B9-4115 
       79.66        12.16         4.18        16.64        21.07        26.40 
TCGA-BQ-7051 TCGA-P4-A5E7 
       50.40        87.09 

$`PTEN WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
      141.73        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.96        84.89        98.33        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.56        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.55         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 
       10.68       100.47       103.40        92.71       104.55       103.10 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
      130.13        99.88       105.60        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      109.91        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4697 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        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        58.45        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-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       38.43        48.82        46.39        56.98        42.41       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        31.66        24.82        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         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        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       17.19        25.55        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        62.86        49.08        44.94        12.23 
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         6.90        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-5168 TCGA-BP-5169 TCGA-BP-5170 
       37.48        35.21        36.23        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        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-5200 TCGA-BP-5201 
       13.41        24.62        33.47        19.82        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-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       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 
       14.63        22.78        62.63        13.28        45.96        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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         7.82         0.23        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 
       34.49        12.46        50.50        28.18        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        99.78        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  PTEN MUTATED PTEN WILD-TYPE 
          3.48           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
        117.80         194.79 
  PTEN MUTATED PTEN WILD-TYPE 
         31.07          37.48 
[1] "3.5 - 117.8 (31.1)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1.1"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED        11        2        11        2
  PTEN WILD-TYPE     314       74       152       86
D3V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I             11            314
  STAGE II             2             74
  STAGE III           11            152
  STAGE IV             2             86
[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    11   2  13   0
  PTEN WILD-TYPE 326  93 208  10
D3V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1           11            326
  T2            2             93
  T3           13            208
  T4            0             10
[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              N0  N1  N2
  PTEN MUTATED    13   3   1
  PTEN WILD-TYPE 259  32   5
D3V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           13            259
  N1            3             32
  N2            1              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus               0   1
  PTEN MUTATED    21   1
  PTEN WILD-TYPE 442  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     21    1
  PTEN WILD-TYPE  442   77
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           21            442
  1            1             77
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  PTEN MUTATED     8  18
  PTEN WILD-TYPE 221 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8   18
  PTEN WILD-TYPE  221  416
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            8            221
  MALE             18            416
[1] 2 2
[1] FALSE
D3V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PTEN MUTATED                    6                                15
  PTEN WILD-TYPE                 60                               421
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PTEN MUTATED                                       5
  PTEN WILD-TYPE                                   156
D3V9, multiclass
                                       clus
vv                                      PTEN MUTATED PTEN WILD-TYPE
  KIDNEY CHROMOPHOBE                               6             60
  KIDNEY CLEAR CELL RENAL CARCINOMA               15            421
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            156
[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, continuous
D3V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     1
  PTEN WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           2    23
  PTEN WILD-TYPE                        64   542
D3V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   2             64
  WHITE                                      23            542
[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"
D3V13, binary
                cls
clus               0   1
  PTEN MUTATED     1  17
  PTEN WILD-TYPE  30 424
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   17
  PTEN WILD-TYPE   30  424
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO           17            424
[1] 2 2
[1] FALSE

Clustering(4) Variable = KDM5C MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    16  12
  KDM5C WILD-TYPE 460 171
  KDM5C MUTATED KDM5C WILD-TYPE 
             28             631 
  KDM5C MUTATED KDM5C WILD-TYPE 
             12             171 
$`KDM5C MUTATED`
TCGA-KL-8345 TCGA-A3-3331 TCGA-AK-3430 TCGA-AK-3458 TCGA-B0-4694 TCGA-B0-4718 
       54.74        48.82        15.78        38.40         3.48        58.45 
TCGA-B0-4816 TCGA-B0-4828 TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-5077 TCGA-B0-5094 
       45.07        10.09        45.30        10.29        43.30        10.95 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5698 TCGA-B2-5641 TCGA-BP-4159 TCGA-BP-4351 
       52.54        58.59       119.38        21.57        85.51        31.89 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5202 TCGA-CJ-4871 
       18.51         6.35        27.02        33.24         0.95        79.66 
TCGA-CW-5581 TCGA-CZ-5467 TCGA-DW-7840 TCGA-HE-A5NH 
       92.02         2.40         3.75        26.01 

$`KDM5C WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 
       49.02        48.59        36.36        37.38        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       73.08       109.41        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        78.64        49.28        94.29        83.21        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       22.45        37.58        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        1.41         4.57         2.53        19.00        65.10         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        52.21        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-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        40.70        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.52        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       36.85        70.52        20.94        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        18.51        15.09         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-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        24.82        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.85         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        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        50.14        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        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        48.53         0.53        34.39        14.30       111.02 
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-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-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         6.90 
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-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-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87        48.10        79.30         1.74        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-5191 
       42.44        37.25        37.22        22.78        13.35        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-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       34.95        31.27       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       75.58        62.66       119.64         7.36        64.57        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       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        21.76        84.30        22.52         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       24.46        13.78        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       17.95        84.89        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
         119.38          194.79 
  KDM5C MUTATED KDM5C WILD-TYPE 
         32.565          37.480 
[1] "0.9 - 119.4 (32.6)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1.8"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        15        1         8        4
  KDM5C WILD-TYPE     310       75       155       84
D4V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              15             310
  STAGE II              1              75
  STAGE III             8             155
  STAGE IV              4              84
[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    15   2  11   0
  KDM5C WILD-TYPE 322  93 210  10
D4V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            15             322
  T2             2              93
  T3            11             210
  T4             0              10
[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               N0  N1  N2
  KDM5C MUTATED    14   1   0
  KDM5C WILD-TYPE 258  34   6
D4V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            14             258
  N1             1              34
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    22   4
  KDM5C WILD-TYPE 441  74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     22    4
  KDM5C WILD-TYPE  441   74
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            22             441
  1             4              74
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     3  25
  KDM5C WILD-TYPE 226 409
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      3   25
  KDM5C WILD-TYPE  226  409
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             3             226
  MALE              25             409
[1] 2 2
[1] FALSE
D4V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              2              91 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KO-8413      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854      TCGA-CZ-4856 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7841      TCGA-DW-7842 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KDM5C MUTATED                    1                                25
  KDM5C WILD-TYPE                 65                               411
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KDM5C MUTATED                                       2
  KDM5C WILD-TYPE                                   159
D4V9, multiclass
                                       clus
vv                                      KDM5C MUTATED KDM5C WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                25             411
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[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, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              50 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433      TCGA-KO-8408 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445      TCGA-AK-3451 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158      TCGA-B8-5164 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
D4V11, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              31 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KM-8639 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409      TCGA-AK-3445 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550      TCGA-A4-A48D 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5C MUTATED                                  0     0
  KDM5C WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED                           2    25
  KDM5C WILD-TYPE                        64   540
D4V12, multiclass
                                  clus
vv                                 KDM5C MUTATED KDM5C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              64
  WHITE                                       25             540
[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"
D4V13, binary
                 cls
clus                0   1
  KDM5C MUTATED     0  21
  KDM5C WILD-TYPE  31 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   21
  KDM5C WILD-TYPE   31  420
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO            21             420
[1] 2 2
[1] FALSE

Clustering(5) Variable = SETD2 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    34  22
  SETD2 WILD-TYPE 442 161
  SETD2 MUTATED SETD2 WILD-TYPE 
             56             603 
  SETD2 MUTATED SETD2 WILD-TYPE 
             22             161 
$`SETD2 MUTATED`
TCGA-KL-8337 TCGA-KM-8438 TCGA-A3-3311 TCGA-A3-3358 TCGA-A3-3367 TCGA-AK-3431 
       44.84       151.96        39.16        42.97        74.63        73.68 
TCGA-AK-3455 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 
       22.45        57.70        43.96        58.45        46.59         5.52 
TCGA-B0-4837 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5098 TCGA-B0-5121 TCGA-B0-5399 
       45.30        36.85        11.90        52.08        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5699 TCGA-B2-4101 TCGA-B4-5835 TCGA-B8-4622 TCGA-BP-4161 
       42.41       126.28        21.30         0.53        50.14        90.28 
TCGA-BP-4329 TCGA-BP-4343 TCGA-BP-4774 TCGA-BP-4790 TCGA-BP-4983 TCGA-BP-5006 
       27.78        62.86        61.97        36.53        46.45        27.62 
TCGA-BP-5169 TCGA-BP-5178 TCGA-BP-5198 TCGA-CJ-4891 TCGA-CJ-5671 TCGA-CJ-5676 
        6.35        62.86        19.82        26.93       131.08       133.71 
TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5580 TCGA-CW-5591 TCGA-CZ-4861 
       18.87       122.83        73.35        64.57        74.66        14.66 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5470 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-A656 
       55.33        10.85        12.69        29.46        12.99        20.32 
TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 
        2.10        86.76        19.27         8.88         7.66         0.95 
TCGA-BQ-7058 TCGA-BQ-7061 
       11.28         7.17 

$`SETD2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 
       73.91        71.41        28.80        54.74        62.37        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       96.62        90.48        92.55        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       51.25        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91       117.80        73.08       109.41        15.78 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       94.29        83.21        28.73        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 
        6.64         3.25        15.72         0.59        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-B0-4838 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-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03         2.27        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        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        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       38.43        56.98       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 
       70.68        85.78        86.47       119.38        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        5.10         0.85         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        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.55        25.91        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        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       48.53         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72       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-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-4341 TCGA-BP-4342 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        74.17        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-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       51.52        63.98       115.69        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       109.84        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 
       51.25       108.56        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-5672 
       38.56        45.14         3.06         4.57        18.81        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
      129.40        25.71        22.32        25.25        18.15        62.10 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
        7.36        92.02        81.83        85.78        66.31        78.18 
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-4862 TCGA-CZ-4863 
        0.59        47.08        69.21        58.75       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5462 
       18.44        79.63        90.54        91.69        94.45        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23        17.23         0.16        14.86 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
       93.34        61.28        50.40        49.84        26.27         7.63 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.04         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.53            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
         151.96          194.79 
  SETD2 MUTATED SETD2 WILD-TYPE 
          42.69           37.25 
[1] "0.5 - 152.0 (42.7)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.5"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        19        7        19       11
  SETD2 WILD-TYPE     306       69       144       77
D5V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              19             306
  STAGE II              7              69
  STAGE III            19             144
  STAGE IV             11              77
[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    21   8  25   2
  SETD2 WILD-TYPE 316  87 196   8
D5V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            21             316
  T2             8              87
  T3            25             196
  T4             2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SETD2 MUTATED    27   2   1
  SETD2 WILD-TYPE 245  33   5
D5V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            27             245
  N1             2              33
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    42  10
  SETD2 WILD-TYPE 421  68
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     42   10
  SETD2 WILD-TYPE  421   68
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            42             421
  1            10              68
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    17  39
  SETD2 WILD-TYPE 212 395
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     17   39
  SETD2 WILD-TYPE  212  395
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            17             212
  MALE              39             395
[1] 2 2
[1] FALSE
D5V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SETD2 MUTATED                    2                                43
  SETD2 WILD-TYPE                 64                               393
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SETD2 MUTATED                                      11
  SETD2 WILD-TYPE                                   150
D5V9, multiclass
                                       clus
vv                                      SETD2 MUTATED SETD2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                43             393
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            11             150
[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, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              50 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-5561 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
D5V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     1
  SETD2 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           6    47
  SETD2 WILD-TYPE                        60   518
D5V12, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    6              60
  WHITE                                       47             518
[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"
D5V13, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  37
  SETD2 WILD-TYPE  30 404
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   37
  SETD2 WILD-TYPE   30  404
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO            37             404
[1] 2 2
[1] FALSE

Clustering(6) Variable = PBRM1 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    91  46
  PBRM1 WILD-TYPE 385 137
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            137             522 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             46             137 
$`PBRM1 MUTATED`
TCGA-A3-3311 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3362 
       39.16        48.59        36.36        37.38        48.82        51.25 
TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3431 TCGA-AK-3434 
       74.63        53.29        20.28       109.91        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4815 
      109.51        38.40        82.45         2.14        58.45        52.21 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4849 
       45.07        16.77        10.09        56.68        26.07         2.27 
TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5104 TCGA-B0-5107 
       36.85        25.32        10.95         2.24        90.48        30.48 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 
       66.05        38.63        52.73        41.88        38.43        46.39 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 
      133.94        15.78        70.68        85.78       119.38       126.28 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       73.84       149.16        79.89       131.15        89.49        91.46 
TCGA-B2-4099 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4148 
       31.96        12.00         5.10         4.64         0.23        27.16 
TCGA-B8-4154 TCGA-B8-5158 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4164 
       45.37        20.91       111.02        85.51        90.28        32.61 
TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4774 TCGA-BP-4801 
       64.27        27.78         0.07        52.24        61.97        36.95 
TCGA-BP-4960 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 
       71.41        61.22        45.50        47.11        36.07        33.34 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4993 TCGA-BP-4995 
       31.30        36.95        27.22         3.88         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5181 
       41.62        48.10         6.35        79.30        74.40        49.15 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5198 
       42.44        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-4875 
       34.95       115.00        46.55        11.05        79.66       116.84 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       30.64        51.52        51.25        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
       38.56         4.57        18.81       133.71        18.87        22.32 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5589 
      122.83        73.35        75.58         7.36        64.57        78.18 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      103.43        25.45        46.16        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 
       79.63        94.45        10.85        84.30        22.52        12.69 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 TCGA-EU-5907 TCGA-A4-7583 
       80.19        12.26        62.63        45.96         4.18         0.10 
TCGA-B1-A656 TCGA-B9-A44B TCGA-BQ-5890 TCGA-BQ-7058 TCGA-BQ-7061 
       20.32         2.10         7.66        11.28         7.17 

$`PBRM1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 
       99.88       105.60        96.62        90.48        92.55        24.16 
TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3370 
       49.02        52.93        45.53        88.37        42.97        74.76 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       43.20        55.76        65.52       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       15.78        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 
       83.21        28.73        22.45        37.58        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
       65.10         5.98        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 
        3.25        15.72        46.59         0.59         5.52        33.50 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
        6.02        36.53        14.93        54.48        29.10        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 
       40.70        45.30        27.42        53.88         6.71        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5075 
       10.29        65.29        39.45        29.03        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5088 
       43.30        11.24        11.90        34.36         7.30        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       15.09         8.05        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5119 
       90.87        52.54        58.59        19.30        52.87        51.02 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5697 
       48.82        56.98        42.41       112.80       129.67        86.47 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5812 
       80.91        71.41       105.37       123.09       130.65       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       32.61        35.90         1.68        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 
       21.57         0.85         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        42.71        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 
       50.14        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 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       14.30        94.72       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
       53.42        62.07        80.68        93.99        18.48        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-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-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 
       10.98        37.25         6.71        47.97         6.94        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4983 
       48.89        49.38         6.90        53.65        14.93        46.45 
TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
       25.81        46.45        16.47        43.00        30.64        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-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       28.87         1.74        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       62.86        38.30        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       58.95        21.24        83.97        49.25        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
      113.46        64.18        63.98       115.69        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       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4918 
       47.67        49.97       108.56        49.28        45.14         3.06 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 
      131.08        72.00       129.40        25.71        25.25        18.15 
TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        67.00       118.85        53.42        62.66       119.64 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
       92.02        81.83        85.78        66.31        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77         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       107.54        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       58.82        90.54        91.69        55.33        10.22        21.76 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        2.40         1.94        31.10        67.96        65.65        14.63 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       22.78        13.28        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-A4-7286 TCGA-A4-7287 
       23.90        18.12         3.91         6.77        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
       61.05        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
       22.06        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.82         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
       49.84        26.27         7.63         7.04         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.16 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         149.16          194.79 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         45.070          35.195 
[1] "0.1 - 149.2 (45.1)" "0.2 - 194.8 (35.2)"
[1] "hr=" "1.2"
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        69       12        35       22
  PBRM1 WILD-TYPE     256       64       128       66
D6V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              69             256
  STAGE II             12              64
  STAGE III            35             128
  STAGE IV             22              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
  PBRM1 MUTATED    70  19  49   0
  PBRM1 WILD-TYPE 267  76 172  10
D6V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            70             267
  T2            19              76
  T3            49             172
  T4             0              10
[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               N0  N1  N2
  PBRM1 MUTATED    63   2   1
  PBRM1 WILD-TYPE 209  33   5
D6V5, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  N0            63             209
  N1             2              33
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   114  22
  PBRM1 WILD-TYPE 349  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    114   22
  PBRM1 WILD-TYPE  349   56
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0           114             349
  1            22              56
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    45  93
  PBRM1 WILD-TYPE 184 341
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     45   93
  PBRM1 WILD-TYPE  184  341
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            45             184
  MALE              93             341
[1] 2 2
[1] FALSE
D6V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PBRM1 MUTATED                    1                               131
  PBRM1 WILD-TYPE                 65                               305
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PBRM1 MUTATED                                       6
  PBRM1 WILD-TYPE                                   155
D6V9, multiclass
                                       clus
vv                                      PBRM1 MUTATED PBRM1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA               131             305
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             6             155
[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, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              2              49 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5164 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792      TCGA-G7-6793 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" 
D6V11, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1              31 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5550      TCGA-A4-A48D 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     1
  PBRM1 WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           5   128
  PBRM1 WILD-TYPE                        61   437
D6V12, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    5              61
  WHITE                                      128             437
[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"
D6V13, binary
                 cls
clus                0   1
  PBRM1 MUTATED     5  91
  PBRM1 WILD-TYPE  26 350
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      5   91
  PBRM1 WILD-TYPE   26  350
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 5              26
  NOT HISPANIC OR LATINO            91             350
[1] 2 2
[1] FALSE

Clustering(7) Variable = NEFH MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    14   2
  NEFH WILD-TYPE 462 181
  NEFH MUTATED NEFH WILD-TYPE 
            16            643 
  NEFH MUTATED NEFH WILD-TYPE 
             2            181 
$`NEFH MUTATED`
TCGA-AK-3451 TCGA-B0-4706 TCGA-B8-4622 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CZ-5456 
       94.29         2.14        50.14        18.15        62.10        79.63 
TCGA-A4-A5DU TCGA-B9-4117 TCGA-B9-A5W8 TCGA-GL-A59T TCGA-HE-A5NK TCGA-HE-A5NL 
       16.31         0.46        17.23        17.95        73.25        25.22 
TCGA-IA-A40X TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5EB 
       19.99        27.78        30.38        99.12 

$`NEFH WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 
        3.48        19.00        65.10         5.98        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        25.91        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       22.32        25.25       122.83        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96         8.48        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 
       50.50        28.18        26.40        20.61        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
        2.10        19.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y 
       84.89        26.01        11.84        56.75        16.80         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       18.41        29.10        34.29        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       87.09        42.94         6.61        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  NEFH MUTATED NEFH WILD-TYPE 
          0.46           0.07 
  NEFH MUTATED NEFH WILD-TYPE 
         99.12         194.79 
  NEFH MUTATED NEFH WILD-TYPE 
         26.50          37.55 
[1] "0.5 - 99.1 (26.5)"  "0.1 - 194.8 (37.5)"
[1] "hr=" "2"  
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         8        3         1        2
  NEFH WILD-TYPE     317       73       162       86
D7V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              8            317
  STAGE II             3             73
  STAGE III            1            162
  STAGE IV             2             86
[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     9   4   3   0
  NEFH WILD-TYPE 328  91 218  10
D7V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            9            328
  T2            4             91
  T3            3            218
  T4            0             10
[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              N0  N1  N2
  NEFH MUTATED     3   0   0
  NEFH WILD-TYPE 269  35   6
D7V5, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  N0            3            269
  N1            0             35
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                cls
clus               0   1
  NEFH MUTATED     6   2
  NEFH WILD-TYPE 457  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      6    2
  NEFH WILD-TYPE  457   76
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            6            457
  1            2             76
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  NEFH MUTATED     4  12
  NEFH WILD-TYPE 225 422
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4   12
  NEFH WILD-TYPE  225  422
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            4            225
  MALE             12            422
[1] 2 2
[1] FALSE
D7V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NEFH MUTATED                    0                                 6
  NEFH WILD-TYPE                 66                               430
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NEFH MUTATED                                      10
  NEFH WILD-TYPE                                   151
D7V9, multiclass
                                       clus
vv                                      NEFH MUTATED NEFH WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                6            430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           10            151
[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, continuous
D7V11, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             30 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AK-3445     TCGA-B8-5158     TCGA-B8-5550     TCGA-A4-A48D 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-A69E     TCGA-DW-5561 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           4    10
  NEFH WILD-TYPE                        62   555
D7V12, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   4             62
  WHITE                                      10            555
[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"
D7V13, binary
                cls
clus               0   1
  NEFH MUTATED     0  13
  NEFH WILD-TYPE  31 428
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0   13
  NEFH WILD-TYPE   31  428
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO           13            428
[1] 2 2
[1] FALSE

Clustering(8) Variable = VHL MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  VHL MUTATED   126  69
  VHL WILD-TYPE 350 114
  VHL MUTATED VHL WILD-TYPE 
          195           464 
  VHL MUTATED VHL WILD-TYPE 
           69           114 
$`VHL MUTATED`
TCGA-KN-8432 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 
        2.50        48.82        45.53        51.25        53.29        55.76 
TCGA-A3-3385 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3455 TCGA-AK-3458 TCGA-B0-4690 
       65.52        78.64        49.28        22.45        38.40         1.41 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        43.96         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       15.72         5.52        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4842 TCGA-B0-4845 
       54.48        29.10        10.09        78.44        56.68        65.29 
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        58.59        38.63        52.73        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5703 
      112.80       129.67       133.94        70.68        85.78        73.84 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
      149.16       130.65        79.89       131.15        91.46       126.05 
TCGA-B2-3924 TCGA-B2-5635 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4148 
       35.90        24.82         5.10         4.64         0.36        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       42.71        25.05        45.37        23.74         1.18        27.02 
TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4166 
       24.23         6.38         0.53        85.51        32.61         0.43 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4349 
       89.36        27.78        18.48        52.24        74.17        12.23 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       31.33        72.59        77.98        44.15        41.75        71.80 
TCGA-BP-4771 TCGA-BP-4789 TCGA-BP-4798 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
        5.33        48.95        10.98         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 
        6.90        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         1.74        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       115.00        63.25        73.22        14.17 
TCGA-CJ-4644 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4892 
       11.05        10.72       116.84        57.83       113.46        50.01 
TCGA-CJ-4894 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
       27.65        56.35        51.25        50.33        54.48        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 
        3.06         4.57       133.71        25.71        25.25        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       67.00       118.85        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 
       64.57        81.83        66.31        74.66        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-5458 TCGA-CZ-5460 
       25.45         0.59        69.21        14.66        91.69        94.45 
TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       84.30        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       12.26        14.63        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-AL-3473 TCGA-BQ-5892 
        4.18        62.66        11.97 

$`VHL WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3357 
       49.02        48.59        36.36        37.38        52.93        88.37 
TCGA-A3-3358 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3425 
       42.97        74.63        74.76        43.20        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
      109.51        94.19        46.78        94.29        83.21        28.73 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4691 
       37.58        82.45        72.89        12.13        40.70         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4718 
        2.53         3.48        19.00        19.73        57.70        58.45 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4836 
       46.59         0.59        52.21        45.07        33.50        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        10.52        10.29 
TCGA-B0-4846 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        66.05        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 
       48.82        46.39        56.98        15.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5712 
      126.28        80.91        71.41       105.37       123.09        89.49 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       32.61         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 
       12.00         0.85         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        50.14        20.91 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
        0.85        50.14        16.60        48.53        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-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-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 
       53.42        62.07        80.68         0.07        93.99        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.84        49.08        44.94        31.89        11.31        33.99 
TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       12.30        77.62         5.98        48.07        13.15        10.82 
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-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        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 
      106.16       114.41        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       49.25        79.66        74.27        75.06        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       66.21        61.91        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        26.93        24.66        39.45       109.84        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4913 
       47.67        49.97       108.56        49.18        49.28        38.56 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       18.81       131.08        72.00       129.40        18.87        22.32 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5585 
       18.15       122.83        62.10        53.42        92.02        85.78 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4859 
       78.18         1.35        18.77        46.16        47.08        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
      107.54        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-5459 
       79.53        23.74        18.44        79.63        90.54        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        22.52         2.40         1.94 
TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       22.78        13.28        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       56.84        23.90        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
        9.63        70.19        66.71        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  VHL MUTATED VHL WILD-TYPE 
         0.36          0.07 
  VHL MUTATED VHL WILD-TYPE 
       149.16        194.79 
  VHL MUTATED VHL WILD-TYPE 
        38.70         36.95 
[1] "0.4 - 149.2 (38.7)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.4"
D8V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED       103       18        45       29
  VHL WILD-TYPE     222       58       118       59
D8V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I           103           222
  STAGE II           18            58
  STAGE III          45           118
  STAGE IV           29            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
  VHL MUTATED   104  22  64   5
  VHL WILD-TYPE 233  73 157   5
D8V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1         104           233
  T2          22            73
  T3          64           157
  T4           5             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  VHL MUTATED    87   5   0
  VHL WILD-TYPE 185  30   6
D8V5, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  N0          87           185
  N1           5            30
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
               cls
clus              0   1
  VHL MUTATED   165  29
  VHL WILD-TYPE 298  49
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    165   29
  VHL WILD-TYPE  298   49
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0         165           298
  1          29            49
[1] 2 2
[1] FALSE
D8V7, binary
               cls
clus              0   1
  VHL MUTATED    74 121
  VHL WILD-TYPE 155 313
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     74  121
  VHL WILD-TYPE  155  313
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          74           155
  MALE           121           313
[1] 2 2
[1] FALSE
D8V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  VHL MUTATED                    1                               192
  VHL WILD-TYPE                 65                               244
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  VHL MUTATED                                       2
  VHL WILD-TYPE                                   159
D8V9, multiclass
                                       clus
vv                                      VHL MUTATED VHL WILD-TYPE
  KIDNEY CHROMOPHOBE                              1            65
  KIDNEY CLEAR CELL RENAL CARCINOMA             192           244
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           2           159
[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, continuous
[1] "Remove cluster labels:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            1            50 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KO-8416    TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-4621    TCGA-B8-5158 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B8-5164    TCGA-B8-5550    TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A44B 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-DW-7963 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-7773 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
D8V11, continuous
[1] "Remove cluster labels:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            1            31 
   TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409    TCGA-AK-3451    TCGA-B8-5158 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B8-5550    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3472 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4117    TCGA-B9-A69E 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7963    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-GL-7773    TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-Q2-A5QZ 
"VHL WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VHL MUTATED                                  0     2
  VHL WILD-TYPE                                2     8
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED                           2   189
  VHL WILD-TYPE                        64   376
D8V12, multiclass
                                  clus
vv                                 VHL MUTATED VHL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      2             8
  BLACK OR AFRICAN AMERICAN                  2            64
  WHITE                                    189           376
[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"
D8V13, binary
               cls
clus              0   1
  VHL MUTATED     8 124
  VHL WILD-TYPE  23 317
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      8  124
  VHL WILD-TYPE   23  317
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               8            23
  NOT HISPANIC OR LATINO         124           317
[1] 2 2
[1] FALSE

Clustering(9) Variable = MET MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  MET MUTATED    16   3
  MET WILD-TYPE 460 180
  MET MUTATED MET WILD-TYPE 
           19           640 
  MET MUTATED MET WILD-TYPE 
            3           180 
$`MET MUTATED`
TCGA-B0-5098 TCGA-B0-5707 TCGA-CW-6087 TCGA-EU-5907 TCGA-A4-7734 TCGA-A4-7997 
       52.08       123.09         1.35         4.18         0.89        30.48 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A654 TCGA-B9-4117 TCGA-BQ-5882 TCGA-BQ-7059 
       66.71        67.73        20.25         0.46        21.63         7.63 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40U TCGA-IZ-8196 
       80.88        74.60        12.43        26.01        16.80        21.34 
TCGA-MH-A561 
       27.65 

$`MET WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       66.31        78.18        74.66        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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-A4-7286 
       56.84        23.90        18.12         3.91         6.77        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        7.82         0.23        16.64        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 
       12.46         9.63        70.19        62.66         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        24.56        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
        3.02        40.77        79.86        51.19        61.02        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       17.95        84.89        11.84        56.75        73.25        25.22 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       19.99         2.04        22.26        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  MET MUTATED MET WILD-TYPE 
         0.46          0.07 
  MET MUTATED MET WILD-TYPE 
       123.09        194.79 
  MET MUTATED MET WILD-TYPE 
       21.630        37.825 
[1] "0.5 - 123.1 (21.6)" "0.1 - 194.8 (37.8)"
[1] "hr=" "1.4"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED        11        0         4        2
  MET WILD-TYPE     314       76       159       86
D9V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I            11           314
  STAGE II            0            76
  STAGE III           4           159
  STAGE IV            2            86
[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
  MET MUTATED    11   2   6   0
  MET WILD-TYPE 326  93 215  10
D9V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1          11           326
  T2           2            93
  T3           6           215
  T4           0            10
[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             N0  N1  N2
  MET MUTATED     5   1   1
  MET WILD-TYPE 267  34   5
D9V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0           5           267
  N1           1            34
  N2           1             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
               cls
clus              0   1
  MET MUTATED     9   1
  MET WILD-TYPE 454  77
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      9    1
  MET WILD-TYPE  454   77
   clus
vv  MET MUTATED MET WILD-TYPE
  0           9           454
  1           1            77
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  MET MUTATED     6  13
  MET WILD-TYPE 223 421
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      6   13
  MET WILD-TYPE  223  421
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           6           223
  MALE            13           421
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            2            91 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KN-8429 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-KN-8434    TCGA-KO-8411    TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-4622 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B8-5158    TCGA-CJ-6028    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-CZ-4861    TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-CZ-5465    TCGA-CZ-5469    TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5906    TCGA-A4-7286    TCGA-A4-7828 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312    TCGA-A4-8517 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-J7-8537 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-Q2-A5QZ 
"MET WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MET MUTATED                    0                                 4
  MET WILD-TYPE                 66                               432
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MET MUTATED                                      15
  MET WILD-TYPE                                   146
D9V9, multiclass
                                       clus
vv                                      MET MUTATED MET WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               4           432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA          15           146
[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, continuous
D9V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           4    11
  MET WILD-TYPE                        62   554
D9V12, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  4            62
  WHITE                                     11           554
[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"
D9V13, binary
               cls
clus              0   1
  MET MUTATED     1  14
  MET WILD-TYPE  30 427
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   14
  MET WILD-TYPE   30  427
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1            30
  NOT HISPANIC OR LATINO          14           427
[1] 2 2
[1] FALSE

Clustering(10) Variable = HNRNPM MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  HNRNPM MUTATED    11   1
  HNRNPM WILD-TYPE 465 182
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              647 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               1              182 
$`HNRNPM MUTATED`
TCGA-KM-8441 TCGA-BP-5010 TCGA-BQ-5887 TCGA-BQ-7055 TCGA-BQ-7062 TCGA-DW-7841 
       28.80        28.87        25.35        26.27         3.81        14.63 
TCGA-DZ-6132 TCGA-EV-5902 TCGA-G7-7502 TCGA-GL-6846 TCGA-IA-A40X TCGA-PJ-A5Z8 
       80.88        19.00        25.84       194.79        19.99        19.73 

$`HNRNPM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 
       49.84        11.28         7.63         7.04         7.17        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        79.86        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        20.52         6.38 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       16.80         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        17.75        14.07 

  HNRNPM MUTATED HNRNPM WILD-TYPE 
            3.81             0.07 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          194.79           151.96 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          25.595           38.070 
[1] "3.8 - 194.8 (25.6)" "0.1 - 152.0 (38.1)"
[1] "hr=" "2.6"
D10V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HNRNPM MUTATED         9        0         2        1
  HNRNPM WILD-TYPE     316       76       161       87
D10V3, multiclass
           clus
vv          HNRNPM MUTATED HNRNPM WILD-TYPE
  STAGE I                9              316
  STAGE II               0               76
  STAGE III              2              161
  STAGE IV               1               87
[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
  HNRNPM MUTATED     9   0   2   1
  HNRNPM WILD-TYPE 328  95 219   9
D10V4, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  T1              9              328
  T2              0               95
  T3              2              219
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HNRNPM MUTATED     2   1   0
  HNRNPM WILD-TYPE 270  34   6
D10V5, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  N0              2              270
  N1              1               34
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     6   0
  HNRNPM WILD-TYPE 457  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      6    0
  HNRNPM WILD-TYPE  457   78
   clus
vv  HNRNPM MUTATED HNRNPM WILD-TYPE
  0              6              457
  1              0               78
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     3   9
  HNRNPM WILD-TYPE 226 425
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      3    9
  HNRNPM WILD-TYPE  226  425
        clus
vv       HNRNPM MUTATED HNRNPM WILD-TYPE
  FEMALE              3              226
  MALE                9              425
[1] 2 2
[1] FALSE
D10V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  HNRNPM MUTATED                    1                                 1
  HNRNPM WILD-TYPE                 65                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  HNRNPM MUTATED                                      10
  HNRNPM WILD-TYPE                                   151
D10V9, multiclass
                                       clus
vv                                      HNRNPM MUTATED HNRNPM WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             10              151
[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, continuous
D10V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPM MUTATED                                  0     0
  HNRNPM WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPM MUTATED                           3     8
  HNRNPM WILD-TYPE                        63   557
D10V12, multiclass
                                  clus
vv                                 HNRNPM MUTATED HNRNPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               63
  WHITE                                         8              557
[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"
D10V13, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     0   8
  HNRNPM WILD-TYPE  31 433
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      0    8
  HNRNPM WILD-TYPE   31  433
                        clus
vv                       HNRNPM MUTATED HNRNPM WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              8              433
[1] 2 2
[1] FALSE

Clustering(11) Variable = NF2 MUTATION ANALYSIS
D11V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    11   5
  NF2 WILD-TYPE 465 178
  NF2 MUTATED NF2 WILD-TYPE 
           16           643 
  NF2 MUTATED NF2 WILD-TYPE 
            5           178 
$`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 
TCGA-A4-8098 TCGA-B1-A47M TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 
       29.46        21.67         0.46        86.76         8.88         2.76 
TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 TCGA-P4-A5EA 
       19.00        25.15         3.68         6.61 

$`NF2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5085 
       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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        49.97        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       19.56        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       28.18        26.40        20.61        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 
       19.23        17.23         0.16        14.86        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       74.60        34.19        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       90.90        11.05        39.25        71.44        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        6.38       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       87.09        42.94        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  NF2 MUTATED NF2 WILD-TYPE 
         0.46          0.07 
  NF2 MUTATED NF2 WILD-TYPE 
        86.76        194.79 
  NF2 MUTATED NF2 WILD-TYPE 
       20.335        38.300 
[1] "0.5 - 86.8 (20.3)"  "0.1 - 194.8 (38.3)"
[1] "hr=" "2.1"
D11V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         4        0         7        4
  NF2 WILD-TYPE     321       76       156       84
D11V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             4           321
  STAGE II            0            76
  STAGE III           7           156
  STAGE IV            4            84
[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     5   1  10   0
  NF2 WILD-TYPE 332  94 211  10
D11V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           5           332
  T2           1            94
  T3          10           211
  T4           0            10
[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             N0  N1  N2
  NF2 MUTATED     1   6   0
  NF2 WILD-TYPE 271  29   6
D11V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           1           271
  N1           6            29
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
               cls
clus              0   1
  NF2 MUTATED     6   4
  NF2 WILD-TYPE 457  74
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      6    4
  NF2 WILD-TYPE  457   74
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           6           457
  1           4            74
[1] 2 2
[1] FALSE
D11V7, binary
               cls
clus              0   1
  NF2 MUTATED     6  10
  NF2 WILD-TYPE 223 424
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      6   10
  NF2 WILD-TYPE  223  424
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           6           223
  MALE            10           424
[1] 2 2
[1] FALSE
D11V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NF2 MUTATED                    0                                 6
  NF2 WILD-TYPE                 66                               430
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NF2 MUTATED                                      10
  NF2 WILD-TYPE                                   151
D11V9, multiclass
                                       clus
vv                                      NF2 MUTATED NF2 WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               6           430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA          10           151
[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, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            50 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KO-8416    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-4621 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B8-5158    TCGA-B8-5164    TCGA-B8-5550    TCGA-A4-8310    TCGA-A4-A48D 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-7268    TCGA-B9-A44B 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-DW-7963 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-7773 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
D11V11, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            31 
   TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409    TCGA-AK-3445    TCGA-AK-3451 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B8-5158    TCGA-B8-5550    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-A69E 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7963    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-7773    TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           5    10
  NF2 WILD-TYPE                        61   555
D11V12, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  5            61
  WHITE                                     10           555
[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"
D11V13, binary
               cls
clus              0   1
  NF2 MUTATED     2  11
  NF2 WILD-TYPE  29 430
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2   11
  NF2 WILD-TYPE   29  430
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               2            29
  NOT HISPANIC OR LATINO          11           430
[1] 2 2
[1] FALSE

Clustering(12) Variable = TDG MUTATION ANALYSIS
D12V1, survival
               sevent
clus2             0   1
  TDG MUTATED     5   0
  TDG WILD-TYPE 471 183
  TDG MUTATED TDG WILD-TYPE 
            5           654 
  TDG MUTATED TDG WILD-TYPE 
            0           183 
$`TDG MUTATED`
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-7840 TCGA-GL-6846 
        0.95        11.97        96.92         3.75       194.79 

$`TDG WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 
       26.04        25.35        13.25        10.82         7.66         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 
       71.44        25.15        20.52        25.84         6.38        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  TDG MUTATED TDG WILD-TYPE 
         0.95          0.07 
  TDG MUTATED TDG WILD-TYPE 
       194.79        151.96 
  TDG MUTATED TDG WILD-TYPE 
        11.97         37.43 
[1] "0.9 - 194.8 (12.0)" "0.1 - 152.0 (37.4)"
[1] "hr="     "3300000"
D12V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TDG MUTATED         3        0         1        1
  TDG WILD-TYPE     322       76       162       87
D12V3, multiclass
           clus
vv          TDG MUTATED TDG WILD-TYPE
  STAGE I             3           322
  STAGE II            0            76
  STAGE III           1           162
  STAGE IV            1            87
[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
  TDG MUTATED     3   0   1   1
  TDG WILD-TYPE 334  95 220   9
D12V4, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  T1           3           334
  T2           0            95
  T3           1           220
  T4           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TDG MUTATED     2   1   0
  TDG WILD-TYPE 270  34   6
D12V5, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  N0           2           270
  N1           1            34
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
               cls
clus              0   1
  TDG MUTATED     3   0
  TDG WILD-TYPE 460  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      3    0
  TDG WILD-TYPE  460   78
   clus
vv  TDG MUTATED TDG WILD-TYPE
  0           3           460
  1           0            78
[1] 2 2
[1] FALSE
D12V7, binary
               cls
clus              0   1
  TDG MUTATED     1   4
  TDG WILD-TYPE 228 430
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    4
  TDG WILD-TYPE  228  430
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1           228
  MALE             4           430
[1] 2 2
[1] FALSE
D12V8, continuous
[1] "Remove cluster labels:" "TDG MUTATED"           
clus
  TDG MUTATED TDG WILD-TYPE 
            1            92 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KN-8429 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-KN-8434    TCGA-KO-8411    TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-4622 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-B8-5158    TCGA-CJ-6028    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-CZ-4861    TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-CZ-5465    TCGA-CZ-5469    TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5906    TCGA-EU-5907    TCGA-A4-7286 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-7828    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"TDG WILD-TYPE" "TDG WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TDG MUTATED                    0                                 0
  TDG WILD-TYPE                 66                               436
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TDG MUTATED                                       5
  TDG WILD-TYPE                                   156
D12V9, multiclass
                                       clus
vv                                      TDG MUTATED TDG WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               0           436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           5           156
[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, continuous
D12V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDG MUTATED                                  0     0
  TDG WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TDG MUTATED                           1     4
  TDG WILD-TYPE                        65   561
D12V12, multiclass
                                  clus
vv                                 TDG MUTATED TDG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            65
  WHITE                                      4           561
[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"
D12V13, binary
               cls
clus              0   1
  TDG MUTATED     0   4
  TDG WILD-TYPE  31 437
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    4
  TDG WILD-TYPE   31  437
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0            31
  NOT HISPANIC OR LATINO           4           437
[1] 2 2
[1] FALSE

Clustering(13) Variable = MUC5B MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  MUC5B MUTATED    24   8
  MUC5B WILD-TYPE 452 175
  MUC5B MUTATED MUC5B WILD-TYPE 
             32             627 
  MUC5B MUTATED MUC5B WILD-TYPE 
              8             175 
$`MUC5B MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8335 TCGA-KL-8339 
       38.07       141.73        90.48       108.62        92.55        28.11 
TCGA-KL-8342 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8416 
       73.91         0.99        52.27       100.47       104.55        90.48 
TCGA-B8-4153 TCGA-BP-4787 TCGA-CJ-4902 TCGA-CW-5580 TCGA-CW-5581 TCGA-DV-5569 
       25.05        15.78        49.97        64.57        92.02        11.67 
TCGA-A4-7288 TCGA-A4-7828 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 
       61.05         7.82        23.97        19.73         8.48         8.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-A47N TCGA-BQ-5888 TCGA-BQ-7044 TCGA-BQ-7062 
       12.99         9.63        24.56        13.25       123.62         3.81 
TCGA-DW-7963 TCGA-P4-A5E7 
       40.77        87.09 

$`MUC5B WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22       137.06       102.81        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.33        96.95        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       24.79        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19       104.52         3.55        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 
      105.47        10.68       103.40        92.71        16.67       103.10 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8417 TCGA-A3-3311 
      130.13        99.88       105.60        96.62        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.16        42.71        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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-4789 
       61.97        60.59        56.91        68.38        11.64        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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        7.36        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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       45.96        12.16        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
        3.91         6.77         4.18        18.21        19.63         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       21.37        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        29.46        25.64        23.28        23.31        19.63 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       14.33        12.46        16.96        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
        7.66         0.95        11.97         7.92         2.76        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.04         7.17        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        99.78        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  MUC5B MUTATED MUC5B WILD-TYPE 
           0.99            0.07 
  MUC5B MUTATED MUC5B WILD-TYPE 
         141.73          194.79 
  MUC5B MUTATED MUC5B WILD-TYPE 
          39.42           37.25 
[1] "1.0 - 141.7 (39.4)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.2"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED        12        5         8        6
  MUC5B WILD-TYPE     313       71       155       82
D13V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I              12             313
  STAGE II              5              71
  STAGE III             8             155
  STAGE IV              6              82
[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
  MUC5B MUTATED    14   6  11   1
  MUC5B WILD-TYPE 323  89 210   9
D13V4, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  T1            14             323
  T2             6              89
  T3            11             210
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MUC5B MUTATED    12   4   0
  MUC5B WILD-TYPE 260  31   6
D13V5, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  N0            12             260
  N1             4              31
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                 cls
clus                0   1
  MUC5B MUTATED    17   5
  MUC5B WILD-TYPE 446  73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     17    5
  MUC5B WILD-TYPE  446   73
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0            17             446
  1             5              73
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  MUC5B MUTATED    13  19
  MUC5B WILD-TYPE 216 415
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     13   19
  MUC5B WILD-TYPE  216  415
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE            13             216
  MALE              19             415
[1] 2 2
[1] FALSE
D13V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MUC5B MUTATED                   12                                 6
  MUC5B WILD-TYPE                 54                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MUC5B MUTATED                                      14
  MUC5B WILD-TYPE                                   147
D13V9, multiclass
                                       clus
vv                                      MUC5B MUTATED MUC5B WILD-TYPE
  KIDNEY CHROMOPHOBE                               12              54
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            14             147
[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, continuous
D13V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC5B MUTATED                                  0     1
  MUC5B WILD-TYPE                                2     9
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC5B MUTATED                           4    27
  MUC5B WILD-TYPE                        62   538
D13V12, multiclass
                                  clus
vv                                 MUC5B MUTATED MUC5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1               9
  BLACK OR AFRICAN AMERICAN                    4              62
  WHITE                                       27             538
[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"
D13V13, binary
                 cls
clus                0   1
  MUC5B MUTATED     1  21
  MUC5B WILD-TYPE  30 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      1   21
  MUC5B WILD-TYPE   30  420
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO            21             420
[1] 2 2
[1] FALSE

Clustering(14) Variable = ZNF814 MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED    12   1
  ZNF814 WILD-TYPE 464 182
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              646 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1              182 
$`ZNF814 MUTATED`
TCGA-KL-8333 TCGA-KL-8344 TCGA-KO-8414 TCGA-BP-5196 TCGA-CJ-5675 TCGA-A4-A5Y1 
       98.33        28.80       105.60        33.47       129.40        12.99 
TCGA-B9-A44B TCGA-DW-7840 TCGA-G7-A4TM TCGA-GL-A4EM TCGA-IZ-8195 TCGA-KV-A6GE 
        2.10         3.75         6.38         1.05        22.26        29.10 
TCGA-P4-A5EB 
       99.12 

$`ZNF814 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       73.91        71.41        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67       104.55       103.10       130.13        99.88        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       90.48        92.55        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       42.97        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       55.76        65.52        20.28       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        78.64        49.28        94.29        83.21        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        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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-5198 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
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 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68        27.65        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       16.80        19.99         2.04        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       12.76        10.55        18.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            1.05             0.07 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          129.40           194.79 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          28.800           37.565 
[1] "1.1 - 129.4 (28.8)" "0.1 - 194.8 (37.6)"
[1] "hr=" "3.3"
D14V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         6        4         3        0
  ZNF814 WILD-TYPE     319       72       160       88
D14V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                6              319
  STAGE II               4               72
  STAGE III              3              160
  STAGE IV               0               88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF814 MUTATED     7   4   2   0
  ZNF814 WILD-TYPE 330  91 219  10
D14V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              7              330
  T2              4               91
  T3              2              219
  T4              0               10
[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                N0  N1  N2
  ZNF814 MUTATED     3   1   0
  ZNF814 WILD-TYPE 269  34   6
D14V5, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  N0              3              269
  N1              1               34
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     5   0
  ZNF814 WILD-TYPE 458  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      5    0
  ZNF814 WILD-TYPE  458   78
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              5              458
  1              0               78
[1] 2 2
[1] FALSE
D14V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     1  12
  ZNF814 WILD-TYPE 228 422
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      1   12
  ZNF814 WILD-TYPE  228  422
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              1              228
  MALE               12              422
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               91 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EU-5907       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7841 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-7502       TCGA-IA-A40U       TCGA-IA-A40X 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZNF814 MUTATED                    3                                 2
  ZNF814 WILD-TYPE                 63                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZNF814 MUTATED                                       8
  ZNF814 WILD-TYPE                                   153
D14V9, multiclass
                                       clus
vv                                      ZNF814 MUTATED ZNF814 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 3               63
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              8              153
[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, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               49 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A48D 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-4117       TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-5561 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-PJ-A5Z9 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" 
D14V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           3    10
  ZNF814 WILD-TYPE                        63   555
D14V12, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               63
  WHITE                                        10              555
[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"
D14V13, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0  10
  ZNF814 WILD-TYPE  31 431
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0   10
  ZNF814 WILD-TYPE   31  431
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO             10              431
[1] 2 2
[1] FALSE

Clustering(15) Variable = CSGALNACT2 MUTATION ANALYSIS
D15V1, survival
                      sevent
clus2                    0   1
  CSGALNACT2 MUTATED     7   0
  CSGALNACT2 WILD-TYPE 469 183
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   7                  652 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   0                  183 
$`CSGALNACT2 MUTATED`
TCGA-KL-8329 TCGA-KL-8334 TCGA-CZ-5984 TCGA-A4-A4ZT TCGA-HE-A5NK TCGA-KV-A6GD 
       90.48        96.95        67.96        16.96        73.25        18.41 
TCGA-MH-A560 
       30.38 

$`CSGALNACT2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        98.33        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       84.89        26.01        11.84        56.75        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 
       12.76        10.55        29.10        34.29        27.78        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               16.96                 0.07 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               96.95               194.79 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
              67.960               37.315 
[1] "17.0 - 97.0 (68.0)" "0.1 - 194.8 (37.3)"
[1] "hr="     "9100000"
D15V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         5        0         2        0
  CSGALNACT2 WILD-TYPE     320       76       161       88
D15V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    5                  320
  STAGE II                   0                   76
  STAGE III                  2                  161
  STAGE IV                   0                   88
[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
  CSGALNACT2 MUTATED     6   0   2   0
  CSGALNACT2 WILD-TYPE 331  95 219  10
D15V4, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                  6                  331
  T2                  0                   95
  T3                  2                  219
  T4                  0                   10
[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                    N0  N1  N2
  CSGALNACT2 MUTATED     3   0   0
  CSGALNACT2 WILD-TYPE 269  35   6
D15V5, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  N0                  3                  269
  N1                  0                   35
  N2                  0                    6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     6   0
  CSGALNACT2 WILD-TYPE 457  78
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      6    0
  CSGALNACT2 WILD-TYPE  457   78
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  6                  457
  1                  0                   78
[1] 2 2
[1] FALSE
D15V7, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     4   4
  CSGALNACT2 WILD-TYPE 225 430
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      4    4
  CSGALNACT2 WILD-TYPE  225  430
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  4                  225
  MALE                    4                  430
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   92 
          TCGA-KM-8438           TCGA-KM-8439           TCGA-KM-8440 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KM-8441           TCGA-KM-8442           TCGA-KM-8443 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KM-8476           TCGA-KM-8477           TCGA-KM-8639 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KN-8429           TCGA-KN-8434           TCGA-KO-8411 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KO-8413           TCGA-AK-3430           TCGA-B0-4838 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B4-5377           TCGA-B4-5832           TCGA-B4-5834 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B4-5835           TCGA-B4-5836           TCGA-B4-5838 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B4-5843           TCGA-B4-5844           TCGA-B8-4143 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B8-4622           TCGA-B8-5158           TCGA-CJ-6028 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-4854           TCGA-CZ-4856           TCGA-CZ-4858 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-4861           TCGA-CZ-4862           TCGA-CZ-5456 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-5457           TCGA-CZ-5458           TCGA-CZ-5465 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-5469           TCGA-CZ-5982           TCGA-DV-5565 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DV-5566           TCGA-DV-5568           TCGA-DV-5569 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DV-5574           TCGA-DV-5575           TCGA-DV-5576 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EU-5904           TCGA-EU-5905           TCGA-EU-5906 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EU-5907           TCGA-A4-7286           TCGA-A4-7828 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8098           TCGA-A4-8310           TCGA-A4-8311 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8312           TCGA-A4-8517           TCGA-A4-8518 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8630           TCGA-A4-A48D           TCGA-A4-A57E 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A5DU           TCGA-A4-A5XZ           TCGA-A4-A6HP 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-AL-3466           TCGA-DW-5560           TCGA-DW-5561 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7834           TCGA-DW-7837           TCGA-DW-7838 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7839           TCGA-DW-7840           TCGA-DW-7841 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7842           TCGA-DW-7963           TCGA-EV-5901 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EV-5902           TCGA-EV-5903           TCGA-G7-6789 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6790           TCGA-G7-6792           TCGA-G7-6793 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6795           TCGA-G7-6796           TCGA-G7-6797 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7501           TCGA-G7-7502           TCGA-G7-A4TM 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IA-A40U           TCGA-IA-A40X           TCGA-IA-A40Y 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-J7-8537           TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
                      vv
clus                   KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CSGALNACT2 MUTATED                    2                                 1
  CSGALNACT2 WILD-TYPE                 64                               435
                      vv
clus                   KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CSGALNACT2 MUTATED                                       5
  CSGALNACT2 WILD-TYPE                                   156
D15V9, multiclass
                                       clus
vv                                      CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                     2                   64
  KIDNEY CLEAR CELL RENAL CARCINOMA                      1                  435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                  5                  156
[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, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   50 
          TCGA-KL-8324           TCGA-KL-8330           TCGA-KL-8335 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KL-8341           TCGA-KL-8345           TCGA-KM-8639 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KN-8428           TCGA-KN-8433           TCGA-KO-8408 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KO-8409           TCGA-KO-8416           TCGA-AK-3445 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-AK-3451           TCGA-B8-4146           TCGA-B8-4621 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B8-5158           TCGA-B8-5164           TCGA-B8-5550 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8310           TCGA-A4-A48D           TCGA-A4-A57E 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A5Y0           TCGA-AL-3466           TCGA-AL-3472 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-AL-7173           TCGA-B1-A654           TCGA-B9-4114 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B9-4115           TCGA-B9-4117           TCGA-B9-7268 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B9-A44B           TCGA-B9-A69E           TCGA-DW-5561 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7834           TCGA-DW-7838           TCGA-DW-7963 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6792           TCGA-G7-6793           TCGA-G7-6795 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7501           TCGA-GL-7773           TCGA-GL-A59T 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-HE-A5NI           TCGA-HE-A5NJ           TCGA-IA-A40U 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IZ-A6M8           TCGA-P4-A5E7           TCGA-P4-A5EB 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-PJ-A5Z9           TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
D15V11, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT2 MUTATED                                  0     1
  CSGALNACT2 WILD-TYPE                                2     9
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT2 MUTATED                           0     5
  CSGALNACT2 WILD-TYPE                        66   560
D15V12, multiclass
                                  clus
vv                                 CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    2
  ASIAN                                             1                    9
  BLACK OR AFRICAN AMERICAN                         0                   66
  WHITE                                             5                  560
[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"
D15V13, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     0   3
  CSGALNACT2 WILD-TYPE  31 438
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    3
  CSGALNACT2 WILD-TYPE   31  438
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                   31
  NOT HISPANIC OR LATINO                  3                  438
[1] 2 2
[1] FALSE

Clustering(16) Variable = GPR50 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2               0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 473 181
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             654 
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             181 
$`GPR50 MUTATED`
TCGA-KN-8436 TCGA-B0-4817 TCGA-DV-5575 TCGA-DV-5576 TCGA-PJ-A5Z9 
       42.35        33.50        56.84        23.90        17.75 

$`GPR50 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 
       46.59         0.59         5.52        52.21        45.07        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       66.28        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       42.94         6.61        99.12        92.58        19.73        14.07 

  GPR50 MUTATED GPR50 WILD-TYPE 
          17.75            0.07 
  GPR50 MUTATED GPR50 WILD-TYPE 
          56.84          194.79 
  GPR50 MUTATED GPR50 WILD-TYPE 
          33.50           37.43 
[1] "17.8 - 56.8 (33.5)" "0.1 - 194.8 (37.4)"
[1] "hr=" "1.7"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GPR50 MUTATED         3        1         1        0
  GPR50 WILD-TYPE     322       75       162       88
D16V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE I               3             322
  STAGE II              1              75
  STAGE III             1             162
  STAGE IV              0              88
[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     3   1   1   0
  GPR50 WILD-TYPE 334  94 220  10
D16V4, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  T1             3             334
  T2             1              94
  T3             1             220
  T4             0              10
[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               N0  N1  N2
  GPR50 MUTATED     1   0   0
  GPR50 WILD-TYPE 271  35   6
D16V5, multiclass
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317      TCGA-A3-3331 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3450 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4823 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5092 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691      TCGA-B0-5692 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5697 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713      TCGA-B2-5633 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4621 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159      TCGA-B8-5163 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545      TCGA-B8-5546 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5553 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160      TCGA-BP-4162 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331      TCGA-BP-4337 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342      TCGA-BP-4343 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351      TCGA-BP-4352 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761      TCGA-BP-4768 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787      TCGA-BP-4795 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799      TCGA-BP-4960 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4986 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995      TCGA-BP-5006 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198      TCGA-BP-5199 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638      TCGA-CJ-4639 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891      TCGA-CJ-4892 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904      TCGA-CJ-4918 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033      TCGA-CW-5585 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4856 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-5451 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456      TCGA-CZ-5467 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984      TCGA-CZ-5985 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-A4-7583 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A5Y1 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656      TCGA-B1-A657 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
D16V6, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   0
  GPR50 WILD-TYPE 460  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    0
  GPR50 WILD-TYPE  460   78
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3             460
  1             0              78
[1] 2 2
[1] FALSE
D16V7, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 226 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    2
  GPR50 WILD-TYPE  226  432
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             3             226
  MALE               2             432
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              2              91 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-EU-5904 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907      TCGA-A4-7286 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GPR50 MUTATED                    1                                 3
  GPR50 WILD-TYPE                 65                               433
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GPR50 MUTATED                                       1
  GPR50 WILD-TYPE                                   160
D16V9, multiclass
                                       clus
vv                                      GPR50 MUTATED GPR50 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[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, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              50 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
D16V11, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              31 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-6793 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR50 MUTATED                                  0     0
  GPR50 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED                           1     4
  GPR50 WILD-TYPE                        65   561
D16V12, multiclass
                                  clus
vv                                 GPR50 MUTATED GPR50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              65
  WHITE                                        4             561
[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"
D16V13, binary
                 cls
clus                0   1
  GPR50 MUTATED     0   5
  GPR50 WILD-TYPE  31 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    5
  GPR50 WILD-TYPE   31  436
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(17) Variable = STAG2 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     9   4
  STAG2 WILD-TYPE 467 179
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             646 
  STAG2 MUTATED STAG2 WILD-TYPE 
              4             179 
$`STAG2 MUTATED`
TCGA-B0-4700 TCGA-B0-5709 TCGA-B0-5712 TCGA-BP-4985 TCGA-BP-5010 TCGA-CJ-4916 
       65.10       130.65        89.49        31.30        28.87        45.14 
TCGA-CZ-4859 TCGA-CZ-5466 TCGA-A4-7287 TCGA-A4-8098 TCGA-B3-4104 TCGA-BQ-5875 
       58.75        22.52        19.63        29.46        34.49        86.76 
TCGA-GL-A4EM 
        1.05 

$`STAG2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        2.53         3.48        19.00         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       123.09        79.89 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        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-5168 TCGA-BP-5169 TCGA-BP-5170 
       37.48        35.21        36.23        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.74        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       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       47.08        69.21        14.66       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        21.76        84.30         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
        4.18        18.21        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       30.58        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        0.16        14.86        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
       27.65        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  STAG2 MUTATED STAG2 WILD-TYPE 
           1.05            0.07 
  STAG2 MUTATED STAG2 WILD-TYPE 
         130.65          194.79 
  STAG2 MUTATED STAG2 WILD-TYPE 
          34.49           37.43 
[1] "1.1 - 130.7 (34.5)" "0.1 - 194.8 (37.4)"
[1] "hr=" "1"  
D17V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         4        1         7        2
  STAG2 WILD-TYPE     321       75       156       86
D17V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               4             321
  STAGE II              1              75
  STAGE III             7             156
  STAGE IV              2              86
[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
  STAG2 MUTATED     4   2   7   1
  STAG2 WILD-TYPE 333  93 214   9
D17V4, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  T1             4             333
  T2             2              93
  T3             7             214
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAG2 MUTATED     4   0   0
  STAG2 WILD-TYPE 268  35   6
D17V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             4             268
  N1             0              35
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                 cls
clus                0   1
  STAG2 MUTATED     9   2
  STAG2 WILD-TYPE 454  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      9    2
  STAG2 WILD-TYPE  454   76
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0             9             454
  1             2              76
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  STAG2 MUTATED     7   7
  STAG2 WILD-TYPE 222 427
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      7    7
  STAG2 WILD-TYPE  222  427
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             7             222
  MALE               7             427
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "STAG2 MUTATED"         
clus
  STAG2 MUTATED STAG2 WILD-TYPE 
              1              92 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  STAG2 MUTATED                    0                                 8
  STAG2 WILD-TYPE                 66                               428
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  STAG2 MUTATED                                       6
  STAG2 WILD-TYPE                                   155
D17V9, multiclass
                                       clus
vv                                      STAG2 MUTATED STAG2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 8             428
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             6             155
[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, continuous
D17V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAG2 MUTATED                                  0     0
  STAG2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED                           2    10
  STAG2 WILD-TYPE                        64   555
D17V12, multiclass
                                  clus
vv                                 STAG2 MUTATED STAG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    2              64
  WHITE                                       10             555
[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"
D17V13, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   9
  STAG2 WILD-TYPE  31 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    9
  STAG2 WILD-TYPE   31  432
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             9             432
[1] 2 2
[1] FALSE

Clustering(18) Variable = NFE2L2 MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     7   3
  NFE2L2 WILD-TYPE 469 180
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              649 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3              180 
$`NFE2L2 MUTATED`
TCGA-B0-4837 TCGA-B0-5097 TCGA-B2-4098 TCGA-BP-4768 TCGA-BP-5178 TCGA-CZ-5456 
       45.30        21.86         1.68        13.15        62.86        79.63 
TCGA-B1-A47M TCGA-BQ-5881 TCGA-BQ-7044 TCGA-BQ-7051 
       21.67        47.80       123.62        50.40 

$`NFE2L2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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-B0-4838 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-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       48.07        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         6.90        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         1.74        74.20        30.64        52.27         9.63 
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       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        19.56        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
        2.76        48.26        96.92        93.34        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1.68             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          123.62           194.79 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           46.55            37.25 
[1] "1.7 - 123.6 (46.5)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1"  
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         4        2         3        1
  NFE2L2 WILD-TYPE     321       74       160       87
D18V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                4              321
  STAGE II               2               74
  STAGE III              3              160
  STAGE IV               1               87
[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
  NFE2L2 MUTATED     4   2   4   0
  NFE2L2 WILD-TYPE 333  93 217  10
D18V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              4              333
  T2              2               93
  T3              4              217
  T4              0               10
[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                N0  N1  N2
  NFE2L2 MUTATED     5   0   0
  NFE2L2 WILD-TYPE 267  35   6
D18V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              5              267
  N1              0               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     8   1
  NFE2L2 WILD-TYPE 455  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      8    1
  NFE2L2 WILD-TYPE  455   77
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              8              455
  1              1               77
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     3   7
  NFE2L2 WILD-TYPE 226 427
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      3    7
  NFE2L2 WILD-TYPE  226  427
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              3              226
  MALE                7              427
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1               92 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5568 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575       TCGA-DV-5576 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NFE2L2 MUTATED                    0                                 6
  NFE2L2 WILD-TYPE                 66                               430
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NFE2L2 MUTATED                                       4
  NFE2L2 WILD-TYPE                                   157
D18V9, multiclass
                                       clus
vv                                      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              157
[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, continuous
D18V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     0
  NFE2L2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           2     8
  NFE2L2 WILD-TYPE                        64   557
D18V12, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               64
  WHITE                                         8              557
[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"
D18V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0   5
  NFE2L2 WILD-TYPE  31 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0    5
  NFE2L2 WILD-TYPE   31  436
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(19) Variable = KDELR3 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  KDELR3 MUTATED     4   2
  KDELR3 WILD-TYPE 472 181
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               6              653 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               2              181 
$`KDELR3 MUTATED`
TCGA-KN-8428 TCGA-KO-8404 TCGA-CJ-4902 TCGA-CZ-5984 TCGA-A4-7915 TCGA-GL-8500 
       52.27        10.68        49.97        67.96         0.23        27.65 

$`KDELR3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        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 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         7.82        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
        3.68         1.05        12.43        17.95        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  KDELR3 MUTATED KDELR3 WILD-TYPE 
            0.23             0.07 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
           67.96           194.79 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
           38.81            37.38 
[1] "0.2 - 68.0 (38.8)"  "0.1 - 194.8 (37.4)"
[1] "hr=" "1.5"
D19V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KDELR3 MUTATED         2        2         1        1
  KDELR3 WILD-TYPE     323       74       162       87
D19V3, multiclass
           clus
vv          KDELR3 MUTATED KDELR3 WILD-TYPE
  STAGE I                2              323
  STAGE II               2               74
  STAGE III              1              162
  STAGE IV               1               87
[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
  KDELR3 MUTATED     2   2   1   1
  KDELR3 WILD-TYPE 335  93 220   9
D19V4, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  T1              2              335
  T2              2               93
  T3              1              220
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  KDELR3 MUTATED     3   0   0
  KDELR3 WILD-TYPE 269  35   6
D19V5, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  N0              3              269
  N1              0               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     2   0
  KDELR3 WILD-TYPE 461  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      2    0
  KDELR3 WILD-TYPE  461   78
   clus
vv  KDELR3 MUTATED KDELR3 WILD-TYPE
  0              2              461
  1              0               78
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     1   5
  KDELR3 WILD-TYPE 228 429
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      1    5
  KDELR3 WILD-TYPE  228  429
        clus
vv       KDELR3 MUTATED KDELR3 WILD-TYPE
  FEMALE              1              228
  MALE                5              429
[1] 2 2
[1] FALSE
D19V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KDELR3 MUTATED                    2                                 2
  KDELR3 WILD-TYPE                 64                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KDELR3 MUTATED                                       2
  KDELR3 WILD-TYPE                                   159
D19V9, multiclass
                                       clus
vv                                      KDELR3 MUTATED KDELR3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[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, continuous
[1] "Remove cluster labels:" "KDELR3 MUTATED"        
clus
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               1               50 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445       TCGA-AK-3451 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158       TCGA-B8-5164 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
D19V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDELR3 MUTATED                                  0     0
  KDELR3 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KDELR3 MUTATED                           1     5
  KDELR3 WILD-TYPE                        65   560
D19V12, multiclass
                                  clus
vv                                 KDELR3 MUTATED KDELR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               65
  WHITE                                         5              560
[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"
D19V13, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     0   5
  KDELR3 WILD-TYPE  31 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      0    5
  KDELR3 WILD-TYPE   31  436
                        clus
vv                       KDELR3 MUTATED KDELR3 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(20) Variable = ATM MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  ATM MUTATED    12   4
  ATM WILD-TYPE 464 179
  ATM MUTATED ATM WILD-TYPE 
           16           643 
  ATM MUTATED ATM WILD-TYPE 
            4           179 
$`ATM MUTATED`
TCGA-KL-8324 TCGA-KN-8428 TCGA-KN-8435 TCGA-B0-5097 TCGA-B0-5703 TCGA-B8-4622 
      141.73        52.27       115.00        21.86        73.84        50.14 
TCGA-BP-4964 TCGA-BP-5173 TCGA-CJ-4639 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-5686 
       61.22         1.74       106.16        56.35       108.56        67.00 
TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 TCGA-A4-7997 
       14.66        63.42        12.26        30.48 

$`ATM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 
       25.91        65.19       104.52         3.55         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 
       19.33         2.50        11.21        59.08        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      104.55       103.10       130.13        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       90.48        92.55        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       42.97        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       55.76        65.52        20.28       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        78.64        49.28        94.29        83.21        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        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       38.43        48.82        46.39        56.98        42.41       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 
      119.38       126.28        80.91        71.41       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       31.66        24.82        21.57        12.00         5.10         0.85 
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        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.55        25.91        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        50.14        16.60         6.38        48.53 
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-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-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-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-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        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         6.90        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-5174 TCGA-BP-5175 
       28.87        48.10         6.35        79.30        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       115.00 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        63.25        73.22        14.17       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45       109.84        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.25        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       47.08        69.21        58.75       107.54        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       61.41        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        67.96        65.65        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
       19.13         0.89         7.82         0.23        16.64        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  ATM MUTATED ATM WILD-TYPE 
         1.74          0.07 
  ATM MUTATED ATM WILD-TYPE 
       141.73        194.79 
  ATM MUTATED ATM WILD-TYPE 
       58.785        37.220 
[1] "1.7 - 141.7 (58.8)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.4"
D20V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         6        6         1        3
  ATM WILD-TYPE     319       70       162       85
D20V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             6           319
  STAGE II            6            70
  STAGE III           1           162
  STAGE IV            3            85
[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     6   6   3   1
  ATM WILD-TYPE 331  89 218   9
D20V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           6           331
  T2           6            89
  T3           3           218
  T4           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ATM MUTATED     9   1   0
  ATM WILD-TYPE 263  34   6
D20V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0           9           263
  N1           1            34
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
               cls
clus              0   1
  ATM MUTATED    11   3
  ATM WILD-TYPE 452  75
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     11    3
  ATM WILD-TYPE  452   75
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          11           452
  1           3            75
[1] 2 2
[1] FALSE
D20V7, binary
               cls
clus              0   1
  ATM MUTATED     7   9
  ATM WILD-TYPE 222 425
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      7    9
  ATM WILD-TYPE  222  425
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           7           222
  MALE             9           425
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            2            91 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KN-8429 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KN-8434    TCGA-KO-8411    TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-5158 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CJ-6028    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4862 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458    TCGA-CZ-5465    TCGA-CZ-5469 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EU-5906    TCGA-EU-5907    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8098 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312    TCGA-A4-8517    TCGA-A4-8518 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-J7-8537 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-Q2-A5QZ 
"ATM WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ATM MUTATED                    3                                12
  ATM WILD-TYPE                 63                               424
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ATM MUTATED                                       1
  ATM WILD-TYPE                                   160
D20V9, multiclass
                                       clus
vv                                      ATM MUTATED ATM WILD-TYPE
  KIDNEY CHROMOPHOBE                              3            63
  KIDNEY CLEAR CELL RENAL CARCINOMA              12           424
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           1           160
[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, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            2            49 
   TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409    TCGA-KO-8416    TCGA-AK-3445 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-4621    TCGA-B8-5158    TCGA-B8-5164 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-5550    TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A69E 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-DW-7963    TCGA-G7-6792 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-7773    TCGA-GL-A59T 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U    TCGA-IZ-A6M8 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
D20V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     0
  ATM WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           0    16
  ATM WILD-TYPE                        66   549
D20V12, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  0            66
  WHITE                                     16           549
[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"
D20V13, binary
               cls
clus              0   1
  ATM MUTATED     1   9
  ATM WILD-TYPE  30 432
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    9
  ATM WILD-TYPE   30  432
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            30
  NOT HISPANIC OR LATINO           9           432
[1] 2 2
[1] FALSE

Clustering(21) Variable = MTOR MUTATION ANALYSIS
D21V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    17  15
  MTOR WILD-TYPE 459 168
  MTOR MUTATED MTOR WILD-TYPE 
            32            627 
  MTOR MUTATED MTOR WILD-TYPE 
            15            168 
$`MTOR MUTATED`
TCGA-KM-8441 TCGA-KN-8437 TCGA-A3-3347 TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 
       28.80       100.87        52.93       109.41        15.72        29.10 
TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5691 
       39.45        36.85        52.08        62.89        51.02       112.80 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5712 TCGA-B4-5832 TCGA-B4-5836 
       85.78        86.47        80.91        89.49         5.10         4.64 
TCGA-B4-5844 TCGA-BP-5175 TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4887 TCGA-CJ-4907 
        0.23        30.64        52.27        11.05        30.64        49.28 
TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5987 
       22.32       118.85        64.57        47.08        61.41        14.63 
TCGA-A4-7828 TCGA-BQ-7061 
        7.82         7.17 

$`MTOR WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38        48.82        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       42.97        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       55.76        65.52        20.28       109.91       117.80        73.08 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       78.64        49.28        94.29        83.21        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        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73        57.70        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        58.45        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       54.48        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03         2.27        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-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        52.87        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5693 
       48.82        46.39        56.98        42.41       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
       15.78        70.68       119.38       126.28        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5834 
       21.30        31.66        24.82        21.57        12.00         0.85 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        0.53         5.46         0.36        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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         1.74        74.20 
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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83       113.46        64.18        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
      108.56        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      133.71        25.71        18.87        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       62.10        73.35        67.00        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
      119.64         7.36        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-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45        46.16         0.59        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
      107.54        63.39         5.46        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        12.26        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.10        21.37        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.04         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  MTOR MUTATED MTOR WILD-TYPE 
          0.23           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        118.85         194.79 
  MTOR MUTATED MTOR WILD-TYPE 
         48.18          37.25 
[1] "0.2 - 118.8 (48.2)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.6"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED        13        3         9        7
  MTOR WILD-TYPE     312       73       154       81
D21V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I             13            312
  STAGE II             3             73
  STAGE III            9            154
  STAGE IV             7             81
[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    14   4  14   0
  MTOR WILD-TYPE 323  91 207  10
D21V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1           14            323
  T2            4             91
  T3           14            207
  T4            0             10
[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              N0  N1  N2
  MTOR MUTATED    15   2   0
  MTOR WILD-TYPE 257  33   6
D21V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           15            257
  N1            2             33
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                cls
clus               0   1
  MTOR MUTATED    23   7
  MTOR WILD-TYPE 440  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     23    7
  MTOR WILD-TYPE  440   71
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           23            440
  1            7             71
[1] 2 2
[1] FALSE
D21V7, binary
                cls
clus               0   1
  MTOR MUTATED    18  14
  MTOR WILD-TYPE 211 420
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     18   14
  MTOR WILD-TYPE  211  420
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           18            211
  MALE             14            420
[1] 2 2
[1] FALSE
D21V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MTOR MUTATED                    2                                28
  MTOR WILD-TYPE                 64                               408
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MTOR MUTATED                                       2
  MTOR WILD-TYPE                                   159
D21V9, multiclass
                                       clus
vv                                      MTOR MUTATED MTOR WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA               28            408
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[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, continuous
D21V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTOR MUTATED                                  0     0
  MTOR WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED                           4    28
  MTOR WILD-TYPE                        62   537
D21V12, multiclass
                                  clus
vv                                 MTOR MUTATED MTOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   4             62
  WHITE                                      28            537
[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"
D21V13, binary
                cls
clus               0   1
  MTOR MUTATED     1  29
  MTOR WILD-TYPE  30 412
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   29
  MTOR WILD-TYPE   30  412
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO           29            412
[1] 2 2
[1] FALSE

Clustering(22) Variable = EGFR MUTATION ANALYSIS
D22V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     2   4
  EGFR WILD-TYPE 474 179
  EGFR MUTATED EGFR WILD-TYPE 
             6            653 
  EGFR MUTATED EGFR WILD-TYPE 
             4            179 
$`EGFR MUTATED`
TCGA-B0-4849 TCGA-B0-5116 TCGA-B0-5713 TCGA-BP-4341 TCGA-BP-4354 TCGA-CJ-4868 
        2.27        41.88        91.46        52.24        33.99        21.24 

$`EGFR WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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-4342 
       62.07        80.68         0.07        93.99        18.48        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-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       11.31        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 
        6.90        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 
        1.74        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       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  EGFR MUTATED EGFR WILD-TYPE 
          2.27           0.07 
  EGFR MUTATED EGFR WILD-TYPE 
         91.46         194.79 
  EGFR MUTATED EGFR WILD-TYPE 
        37.935         37.380 
[1] "2.3 - 91.5 (37.9)"  "0.1 - 194.8 (37.4)"
[1] "hr=" "2.6"
D22V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EGFR MUTATED         0        0         4        2
  EGFR WILD-TYPE     325       76       159       86
D22V3, multiclass
           clus
vv          EGFR MUTATED EGFR WILD-TYPE
  STAGE I              0            325
  STAGE II             0             76
  STAGE III            4            159
  STAGE IV             2             86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED     0   0   5   1
  EGFR WILD-TYPE 337  95 216   9
D22V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            0            337
  T2            0             95
  T3            5            216
  T4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EGFR MUTATED     3   1   0
  EGFR WILD-TYPE 269  34   6
D22V5, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  N0            3            269
  N1            1             34
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                cls
clus               0   1
  EGFR MUTATED     4   2
  EGFR WILD-TYPE 459  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      4    2
  EGFR WILD-TYPE  459   76
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            4            459
  1            2             76
[1] 2 2
[1] FALSE
D22V7, binary
                cls
clus               0   1
  EGFR MUTATED     1   5
  EGFR WILD-TYPE 228 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      1    5
  EGFR WILD-TYPE  228  429
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            1            228
  MALE              5            429
[1] 2 2
[1] FALSE
D22V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  EGFR MUTATED                    0                                 6
  EGFR WILD-TYPE                 66                               430
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  EGFR MUTATED                                       0
  EGFR WILD-TYPE                                   161
D22V9, multiclass
                                       clus
vv                                      EGFR MUTATED EGFR WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                6            430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            0            161
[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, continuous
D22V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     0
  EGFR WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           0     6
  EGFR WILD-TYPE                        66   559
D22V12, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             66
  WHITE                                       6            559
[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"
D22V13, binary
                cls
clus               0   1
  EGFR MUTATED     0   4
  EGFR WILD-TYPE  31 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0    4
  EGFR WILD-TYPE   31  437
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            4            437
[1] 2 2
[1] FALSE

Clustering(23) Variable = SLC6A14 MUTATION ANALYSIS
D23V1, survival
                   sevent
clus2                 0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE 473 181
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               654 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2               181 
$`SLC6A14 MUTATED`
TCGA-KO-8416 TCGA-BP-4972 TCGA-BP-4985 TCGA-G7-6789 TCGA-P4-A5E7 
       90.48        49.38        31.30         4.01        87.09 

$`SLC6A14 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
       99.88       105.60        96.62        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        45.50         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       24.89        10.68        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 
       27.78        30.38        27.65        20.25        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
             4.01              0.07 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
            90.48            194.79 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
           49.380            37.315 
[1] "4.0 - 90.5 (49.4)"  "0.1 - 194.8 (37.3)"
[1] "hr=" "1.2"
D23V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC6A14 MUTATED         1        0         3        1
  SLC6A14 WILD-TYPE     324       76       160       87
D23V3, multiclass
           clus
vv          SLC6A14 MUTATED SLC6A14 WILD-TYPE
  STAGE I                 1               324
  STAGE II                0                76
  STAGE III               3               160
  STAGE IV                1                87
[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
  SLC6A14 MUTATED     1   0   4   0
  SLC6A14 WILD-TYPE 336  95 217  10
D23V4, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  T1               1               336
  T2               0                95
  T3               4               217
  T4               0                10
[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                 N0  N1  N2
  SLC6A14 MUTATED     2   0   1
  SLC6A14 WILD-TYPE 270  35   5
D23V5, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  N0               2               270
  N1               0                35
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   0
  SLC6A14 WILD-TYPE 460  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    0
  SLC6A14 WILD-TYPE  460   78
   clus
vv  SLC6A14 MUTATED SLC6A14 WILD-TYPE
  0               3               460
  1               0                78
[1] 2 2
[1] FALSE
D23V7, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE 226 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    2
  SLC6A14 WILD-TYPE  226  432
        clus
vv       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  FEMALE               3               226
  MALE                 2               432
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "SLC6A14 MUTATED"       
clus
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                1                92 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8411 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KO-8413        TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4854 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-4862 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-EU-5907        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6792 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-IA-A40U 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC6A14 MUTATED                    1                                 2
  SLC6A14 WILD-TYPE                 65                               434
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC6A14 MUTATED                                       2
  SLC6A14 WILD-TYPE                                   159
D23V9, multiclass
                                       clus
vv                                      SLC6A14 MUTATED SLC6A14 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               159
[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, continuous
[1] "Remove cluster labels:" "SLC6A14 MUTATED"       
clus
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2                49 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-AK-3445        TCGA-AK-3451 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158        TCGA-B8-5164 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B8-5550        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7838        TCGA-DW-7963        TCGA-G7-6792 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7773 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IZ-A6M8        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-Q2-A5QZ 
"SLC6A14 WILD-TYPE" 
D23V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A14 MUTATED                                  0     0
  SLC6A14 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC6A14 MUTATED                           0     5
  SLC6A14 WILD-TYPE                        66   560
D23V12, multiclass
                                  clus
vv                                 SLC6A14 MUTATED SLC6A14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                66
  WHITE                                          5               560
[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"
D23V13, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     0   3
  SLC6A14 WILD-TYPE  31 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      0    3
  SLC6A14 WILD-TYPE   31  438
                        clus
vv                       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  HISPANIC OR LATINO                   0                31
  NOT HISPANIC OR LATINO               3               438
[1] 2 2
[1] FALSE

Clustering(24) Variable = PIK3CA MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     8   4
  PIK3CA WILD-TYPE 468 179
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              647 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4              179 
$`PIK3CA MUTATED`
TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-5713 TCGA-B8-5159 TCGA-BP-4160 TCGA-BP-4352 
       88.37         2.53        91.46        23.74        94.72        11.31 
TCGA-BP-4960 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 TCGA-BQ-5893 TCGA-DZ-6134 
       71.41        74.27        64.18         7.36         7.92        61.02 

$`PIK3CA WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       72.89        12.13        40.70         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        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        20.91 
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        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        48.53         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        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-4354 
       49.84        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-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-4961 
       37.25        36.95         6.71        47.97         6.94        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         6.90        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         1.74        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 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        79.66        10.72        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83       113.46        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95        11.97         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           94.72           194.79 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           62.60            37.25 
[1] "2.5 - 94.7 (62.6)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "1.1"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         3        2         4        3
  PIK3CA WILD-TYPE     322       74       159       85
D24V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                3              322
  STAGE II               2               74
  STAGE III              4              159
  STAGE IV               3               85
[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     3   2   7   0
  PIK3CA WILD-TYPE 334  93 214  10
D24V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              3              334
  T2              2               93
  T3              7              214
  T4              0               10
[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                N0  N1  N2
  PIK3CA MUTATED     9   1   0
  PIK3CA WILD-TYPE 263  34   6
D24V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0              9              263
  N1              1               34
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   3
  PIK3CA WILD-TYPE 455  75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    3
  PIK3CA WILD-TYPE  455   75
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              8              455
  1              3               75
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7   5
  PIK3CA WILD-TYPE 222 429
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    5
  PIK3CA WILD-TYPE  222  429
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              7              222
  MALE                5              429
[1] 2 2
[1] FALSE
D24V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PIK3CA MUTATED                    0                                10
  PIK3CA WILD-TYPE                 66                               426
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PIK3CA MUTATED                                       2
  PIK3CA WILD-TYPE                                   159
D24V9, multiclass
                                       clus
vv                                      PIK3CA MUTATED PIK3CA WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 10              426
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[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, continuous
D24V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           0    12
  PIK3CA WILD-TYPE                        66   553
D24V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               66
  WHITE                                        12              553
[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"
D24V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1   9
  PIK3CA WILD-TYPE  30 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    9
  PIK3CA WILD-TYPE   30  432
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               30
  NOT HISPANIC OR LATINO              9              432
[1] 2 2
[1] FALSE

Clustering(25) Variable = EMG1 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 472 183
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            655 
  EMG1 MUTATED EMG1 WILD-TYPE 
             0            183 
$`EMG1 MUTATED`
TCGA-AK-3427 TCGA-AK-3440 TCGA-AS-3777 TCGA-BP-5186 
      117.80        94.19        40.70        22.78 

$`EMG1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      109.91        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
      109.51        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       12.13         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        37.22        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  EMG1 MUTATED EMG1 WILD-TYPE 
         22.78           0.07 
  EMG1 MUTATED EMG1 WILD-TYPE 
        117.80         194.79 
  EMG1 MUTATED EMG1 WILD-TYPE 
        67.445         37.250 
[1] "22.8 - 117.8 (67.4)" "0.1 - 194.8 (37.2)" 
[1] "hr="     "3300000"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EMG1 MUTATED         4        0         0        0
  EMG1 WILD-TYPE     321       76       163       88
D25V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              4            321
  STAGE II             0             76
  STAGE III            0            163
  STAGE IV             0             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EMG1 MUTATED     4   0   0   0
  EMG1 WILD-TYPE 333  95 221  10
D25V4, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T1            4            333
  T2            0             95
  T3            0            221
  T4            0             10
[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              N0  N1  N2
  EMG1 MUTATED     2   0   0
  EMG1 WILD-TYPE 270  35   6
D25V5, multiclass
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            311 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3313     TCGA-A3-3317     TCGA-A3-3331 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385     TCGA-A3-3387 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3428     TCGA-AK-3429     TCGA-AK-3430 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3450     TCGA-AK-3451 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5092 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691     TCGA-B0-5692 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620     TCGA-B8-4621 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159     TCGA-B8-5163 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545     TCGA-B8-5546 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5553 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160     TCGA-BP-4162 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331     TCGA-BP-4337 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342     TCGA-BP-4343 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4795 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799     TCGA-BP-4960 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4986 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995     TCGA-BP-5006 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-5191     TCGA-BP-5198     TCGA-BP-5199     TCGA-BP-5201 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4636     TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4890     TCGA-CJ-4891     TCGA-CJ-4892     TCGA-CJ-4894 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4900     TCGA-CJ-4904     TCGA-CJ-4918     TCGA-CJ-5678 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-6030     TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4857 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451     TCGA-CZ-5452 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467     TCGA-CZ-5469 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583     TCGA-A4-7585 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1     TCGA-AL-3466 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657     TCGA-B9-7268 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058     TCGA-DW-7963 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-A59R 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
D25V6, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 459  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  459   78
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            459
  1            0             78
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus               0   1
  EMG1 MUTATED     1   3
  EMG1 WILD-TYPE 228 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      1    3
  EMG1 WILD-TYPE  228  431
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            1            228
  MALE              3            431
[1] 2 2
[1] FALSE
D25V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  EMG1 MUTATED                    0                                 4
  EMG1 WILD-TYPE                 66                               432
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  EMG1 MUTATED                                       0
  EMG1 WILD-TYPE                                   161
D25V9, multiclass
                                       clus
vv                                      EMG1 MUTATED EMG1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                4            432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            0            161
[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, continuous
D25V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     4
  EMG1 WILD-TYPE                        66   561
D25V12, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             66
  WHITE                                       4            561
[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"
D25V13, binary
                cls
clus               0   1
  EMG1 MUTATED     0   3
  EMG1 WILD-TYPE  31 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    3
  EMG1 WILD-TYPE   31  438
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(26) Variable = RIMBP3 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     2   3
  RIMBP3 WILD-TYPE 474 180
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              654 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               3              180 
$`RIMBP3 MUTATED`
TCGA-KO-8404 TCGA-KO-8409 TCGA-B0-4945 TCGA-BP-4164 TCGA-BP-4964 
       10.68       104.55        70.52        32.61        61.22 

$`RIMBP3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35       100.87       105.47       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        36.85        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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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-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-4965 
        6.94        71.41        63.62        58.68        60.30        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 
        6.90        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 
        1.74        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       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
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 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           10.68             0.07 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          104.55           194.79 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          61.220           37.315 
[1] "10.7 - 104.5 (61.2)" "0.1 - 194.8 (37.3)" 
[1] "hr=" "1.8"
D26V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RIMBP3 MUTATED         2        1         1        1
  RIMBP3 WILD-TYPE     323       75       162       87
D26V3, multiclass
           clus
vv          RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                2              323
  STAGE II               1               75
  STAGE III              1              162
  STAGE IV               1               87
[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
  RIMBP3 MUTATED     2   1   1   1
  RIMBP3 WILD-TYPE 335  94 220   9
D26V4, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              2              335
  T2              1               94
  T3              1              220
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RIMBP3 MUTATED     3   0   0
  RIMBP3 WILD-TYPE 269  35   6
D26V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              3              269
  N1              0               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   0
  RIMBP3 WILD-TYPE 459  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    0
  RIMBP3 WILD-TYPE  459   78
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              4              459
  1              0               78
[1] 2 2
[1] FALSE
D26V7, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     3   2
  RIMBP3 WILD-TYPE 226 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      3    2
  RIMBP3 WILD-TYPE  226  432
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  FEMALE              3              226
  MALE                2              432
[1] 2 2
[1] FALSE
D26V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RIMBP3 MUTATED                    2                                 3
  RIMBP3 WILD-TYPE                 64                               433
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RIMBP3 MUTATED                                       0
  RIMBP3 WILD-TYPE                                   161
D26V9, multiclass
                                       clus
vv                                      RIMBP3 MUTATED RIMBP3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  3              433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              0              161
[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, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               50 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8416       TCGA-AK-3445       TCGA-AK-3451 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158       TCGA-B8-5164 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
D26V11, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               31 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-AK-3445 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550       TCGA-A4-A48D 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793       TCGA-G7-6795 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMBP3 MUTATED                                  0     0
  RIMBP3 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RIMBP3 MUTATED                           0     5
  RIMBP3 WILD-TYPE                        66   560
D26V12, multiclass
                                  clus
vv                                 RIMBP3 MUTATED RIMBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               66
  WHITE                                         5              560
[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"
D26V13, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     0   3
  RIMBP3 WILD-TYPE  31 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      0    3
  RIMBP3 WILD-TYPE   31  438
                        clus
vv                       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              3              438
[1] 2 2
[1] FALSE

Clustering(27) Variable = RAI1 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  RAI1 MUTATED     5   2
  RAI1 WILD-TYPE 471 181
  RAI1 MUTATED RAI1 WILD-TYPE 
             7            652 
  RAI1 MUTATED RAI1 WILD-TYPE 
             2            181 
$`RAI1 MUTATED`
TCGA-KN-8431 TCGA-KO-8404 TCGA-B0-5077 TCGA-CJ-4904 TCGA-DV-5575 TCGA-A4-8630 
       19.33        10.68        43.30       108.56        56.84        14.33 
TCGA-B1-A656 
       20.32 

$`RAI1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 
       29.03         2.27        36.85        70.52        20.94        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.25        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 
       13.28        45.96        12.16        11.67        66.28        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D 
       23.97        23.28        23.31        19.63        19.73        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  RAI1 MUTATED RAI1 WILD-TYPE 
         10.68           0.07 
  RAI1 MUTATED RAI1 WILD-TYPE 
        108.56         194.79 
  RAI1 MUTATED RAI1 WILD-TYPE 
         20.32          37.43 
[1] "10.7 - 108.6 (20.3)" "0.1 - 194.8 (37.4)" 
[1] "hr=" "1.2"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RAI1 MUTATED         4        1         0        2
  RAI1 WILD-TYPE     321       75       163       86
D27V3, multiclass
           clus
vv          RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I              4            321
  STAGE II             1             75
  STAGE III            0            163
  STAGE IV             2             86
[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
  RAI1 MUTATED     4   1   1   1
  RAI1 WILD-TYPE 333  94 220   9
D27V4, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  T1            4            333
  T2            1             94
  T3            1            220
  T4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RAI1 MUTATED     3   0   0
  RAI1 WILD-TYPE 269  35   6
D27V5, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  N0            3            269
  N1            0             35
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                cls
clus               0   1
  RAI1 MUTATED     3   1
  RAI1 WILD-TYPE 460  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      3    1
  RAI1 WILD-TYPE  460   77
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0            3            460
  1            1             77
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  RAI1 MUTATED     4   3
  RAI1 WILD-TYPE 225 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      4    3
  RAI1 WILD-TYPE  225  431
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE            4            225
  MALE              3            431
[1] 2 2
[1] FALSE
D27V8, continuous
[1] "Remove cluster labels:" "RAI1 MUTATED"          
clus
  RAI1 MUTATED RAI1 WILD-TYPE 
             2             91 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8411 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KO-8413     TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4854 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5576 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906     TCGA-EU-5907 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-5560 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RAI1 MUTATED                    2                                 3
  RAI1 WILD-TYPE                 64                               433
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RAI1 MUTATED                                       2
  RAI1 WILD-TYPE                                   159
D27V9, multiclass
                                       clus
vv                                      RAI1 MUTATED RAI1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                3            433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[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, continuous
D27V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAI1 MUTATED                                  0     0
  RAI1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAI1 MUTATED                           0     6
  RAI1 WILD-TYPE                        66   559
D27V12, multiclass
                                  clus
vv                                 RAI1 MUTATED RAI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             66
  WHITE                                       6            559
[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"
D27V13, binary
                cls
clus               0   1
  RAI1 MUTATED     0   6
  RAI1 WILD-TYPE  31 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      0    6
  RAI1 WILD-TYPE   31  435
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            6            435
[1] 2 2
[1] FALSE

Clustering(28) Variable = FAM160B2 MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  FAM160B2 MUTATED     2   2
  FAM160B2 WILD-TYPE 474 181
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                655 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 2                181 
$`FAM160B2 MUTATED`
TCGA-KM-8441 TCGA-B0-4816 TCGA-CJ-5677 TCGA-A4-7997 
       28.80        45.07        25.71        30.48 

$`FAM160B2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        52.21        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        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       131.08        72.00       129.40       133.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
       19.13         0.89         7.82         0.23        16.64        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             25.71               0.07 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             45.07             194.79 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             29.64              37.48 
[1] "25.7 - 45.1 (29.6)" "0.1 - 194.8 (37.5)"
[1] "hr=" "2.3"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  FAM160B2 MUTATED         2        1         0        1
  FAM160B2 WILD-TYPE     323       75       163       87
D28V3, multiclass
           clus
vv          FAM160B2 MUTATED FAM160B2 WILD-TYPE
  STAGE I                  2                323
  STAGE II                 1                 75
  STAGE III                0                163
  STAGE IV                 1                 87
[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
  FAM160B2 MUTATED     2   1   1   0
  FAM160B2 WILD-TYPE 335  94 220  10
D28V4, multiclass
    clus
vv   FAM160B2 MUTATED FAM160B2 WILD-TYPE
  T1                2                335
  T2                1                 94
  T3                1                220
  T4                0                 10
[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                  N0  N1  N2
  FAM160B2 MUTATED     1   0   0
  FAM160B2 WILD-TYPE 271  35   6
D28V5, multiclass
[1] "Remove cluster labels:" "FAM160B2 MUTATED"      
clus
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 1                312 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8443         TCGA-KN-8418 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8430         TCGA-KO-8405         TCGA-KO-8406 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8407         TCGA-KO-8408         TCGA-KO-8409 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8410         TCGA-KO-8413         TCGA-KO-8414 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3317         TCGA-A3-3331 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3357 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3358         TCGA-A3-3362         TCGA-A3-3367 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3370         TCGA-A3-3373         TCGA-A3-3374 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3376         TCGA-A3-3385         TCGA-A3-3387 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3425         TCGA-AK-3427         TCGA-AK-3428 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3429         TCGA-AK-3430         TCGA-AK-3436 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3443         TCGA-AK-3450         TCGA-AK-3451 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3456         TCGA-B0-4690         TCGA-B0-4691 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4693         TCGA-B0-4703         TCGA-B0-4710 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4810         TCGA-B0-4811         TCGA-B0-4814 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4817         TCGA-B0-4823         TCGA-B0-4824 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4827         TCGA-B0-4833         TCGA-B0-4837 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4838         TCGA-B0-4839         TCGA-B0-4842 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4843         TCGA-B0-4846         TCGA-B0-4852 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4945         TCGA-B0-5075         TCGA-B0-5077 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5080         TCGA-B0-5081         TCGA-B0-5083 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5084         TCGA-B0-5085         TCGA-B0-5088 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5092         TCGA-B0-5094         TCGA-B0-5095 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5096         TCGA-B0-5097         TCGA-B0-5104 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5106         TCGA-B0-5107         TCGA-B0-5108 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5109         TCGA-B0-5110         TCGA-B0-5113 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5115         TCGA-B0-5116         TCGA-B0-5119 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5120         TCGA-B0-5121         TCGA-B0-5399 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5400         TCGA-B0-5691         TCGA-B0-5692 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5694         TCGA-B0-5695         TCGA-B0-5696 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5697         TCGA-B0-5698         TCGA-B0-5699 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5701         TCGA-B0-5702         TCGA-B0-5703 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5705         TCGA-B0-5706         TCGA-B0-5707 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5710         TCGA-B0-5712         TCGA-B0-5713 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5641         TCGA-B4-5377 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4148 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-4620         TCGA-B8-4621         TCGA-B8-4622 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5159         TCGA-B8-5163 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5164         TCGA-B8-5165         TCGA-B8-5545 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5546         TCGA-B8-5549         TCGA-B8-5550 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5551         TCGA-B8-5553         TCGA-BP-4158 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4159         TCGA-BP-4160         TCGA-BP-4162 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4165         TCGA-BP-4166 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4169         TCGA-BP-4170         TCGA-BP-4173 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4174         TCGA-BP-4326         TCGA-BP-4329 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4330         TCGA-BP-4331         TCGA-BP-4337 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4338         TCGA-BP-4340         TCGA-BP-4342 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4343         TCGA-BP-4345         TCGA-BP-4346 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4351         TCGA-BP-4352         TCGA-BP-4354 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4756         TCGA-BP-4761         TCGA-BP-4768 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4770         TCGA-BP-4771         TCGA-BP-4787 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4795         TCGA-BP-4797         TCGA-BP-4798 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4799         TCGA-BP-4960         TCGA-BP-4964 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4967         TCGA-BP-4968         TCGA-BP-4970 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4971         TCGA-BP-4974         TCGA-BP-4985 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4986         TCGA-BP-4988         TCGA-BP-4989 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4995         TCGA-BP-5006         TCGA-BP-5007 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5010         TCGA-BP-5169         TCGA-BP-5182 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5186         TCGA-BP-5191         TCGA-BP-5198 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5199         TCGA-BP-5201         TCGA-CJ-4636 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644         TCGA-CJ-4868 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4869         TCGA-CJ-4872         TCGA-CJ-4873 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4874         TCGA-CJ-4876         TCGA-CJ-4890 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4891         TCGA-CJ-4892         TCGA-CJ-4894 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4900         TCGA-CJ-4904         TCGA-CJ-4918 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-5678         TCGA-CJ-6030         TCGA-CJ-6033 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CW-5585         TCGA-CW-5591         TCGA-CW-6087 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-CZ-4857 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4859         TCGA-CZ-4863         TCGA-CZ-5451 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5454         TCGA-CZ-5456 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5469         TCGA-CZ-5470 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5988         TCGA-CZ-5989         TCGA-A4-7583 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7915         TCGA-A4-A57E 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-AL-3466         TCGA-AL-3472 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7058         TCGA-DW-7963 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-IA-A40U 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-6720         TCGA-J7-8537 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
D28V6, binary
                    cls
clus                   0   1
  FAM160B2 MUTATED     2   1
  FAM160B2 WILD-TYPE 461  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      2    1
  FAM160B2 WILD-TYPE  461   77
   clus
vv  FAM160B2 MUTATED FAM160B2 WILD-TYPE
  0                2                461
  1                1                 77
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  FAM160B2 MUTATED     2   2
  FAM160B2 WILD-TYPE 227 432
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      2    2
  FAM160B2 WILD-TYPE  227  432
        clus
vv       FAM160B2 MUTATED FAM160B2 WILD-TYPE
  FEMALE                2                227
  MALE                  2                432
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "FAM160B2 MUTATED"      
clus
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 1                 92 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KN-8429 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8434         TCGA-KO-8411         TCGA-KO-8413 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3430         TCGA-B0-4838         TCGA-B4-5377 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4622 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5158         TCGA-CJ-6028         TCGA-CZ-4854 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4861 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5465         TCGA-CZ-5469 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5982         TCGA-DV-5565         TCGA-DV-5566 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5574 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-EU-5904 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7842         TCGA-DW-7963         TCGA-EV-5901 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40X         TCGA-IA-A40Y 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-J7-8537         TCGA-Q2-A5QZ 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM160B2 MUTATED                    1                                 2
  FAM160B2 WILD-TYPE                 65                               434
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM160B2 MUTATED                                       1
  FAM160B2 WILD-TYPE                                   160
D28V9, multiclass
                                       clus
vv                                      FAM160B2 MUTATED FAM160B2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                    2                434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                160
[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, continuous
D28V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM160B2 MUTATED                                  0     0
  FAM160B2 WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  FAM160B2 MUTATED                           0     4
  FAM160B2 WILD-TYPE                        66   561
D28V12, multiclass
                                  clus
vv                                 FAM160B2 MUTATED FAM160B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 10
  BLACK OR AFRICAN AMERICAN                       0                 66
  WHITE                                           4                561
[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"
D28V13, binary
                    cls
clus                   0   1
  FAM160B2 MUTATED     0   4
  FAM160B2 WILD-TYPE  31 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      0    4
  FAM160B2 WILD-TYPE   31  437
                        clus
vv                       FAM160B2 MUTATED FAM160B2 WILD-TYPE
  HISPANIC OR LATINO                    0                 31
  NOT HISPANIC OR LATINO                4                437
[1] 2 2
[1] FALSE

Clustering(29) Variable = ZNF598 MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  ZNF598 MUTATED     7   3
  ZNF598 WILD-TYPE 469 180
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              649 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               3              180 
$`ZNF598 MUTATED`
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B3-8121 TCGA-BQ-5877 TCGA-BQ-5893 TCGA-DW-7834 
       62.66         2.20        12.46         8.88         7.92       129.86 
TCGA-DW-7838 TCGA-EV-5903 TCGA-G7-7501 TCGA-G7-7502 
       24.46        24.89        20.52        25.84 

$`ZNF598 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 
       12.46         9.63        70.19        66.71        67.73        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       33.83        10.09        30.58        34.49        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95        11.97         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       13.61        37.55        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       34.19        19.00        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-GL-6846 
       11.05        39.25        71.44        25.15         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
            2.20             0.07 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          129.86           194.79 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           22.49            37.58 
[1] "2.2 - 129.9 (22.5)" "0.1 - 194.8 (37.6)"
[1] "hr=" "1.6"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         7        1         1        2
  ZNF598 WILD-TYPE     318       75       162       86
D29V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                7              318
  STAGE II               1               75
  STAGE III              1              162
  STAGE IV               2               86
[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
  ZNF598 MUTATED     7   1   3   0
  ZNF598 WILD-TYPE 330  94 218  10
D29V4, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  T1              7              330
  T2              1               94
  T3              3              218
  T4              0               10
[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                N0  N1  N2
  ZNF598 MUTATED     2   3   0
  ZNF598 WILD-TYPE 270  32   6
D29V5, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  N0              2              270
  N1              3               32
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   2
  ZNF598 WILD-TYPE 461  76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    2
  ZNF598 WILD-TYPE  461   76
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0              2              461
  1              2               76
[1] 2 2
[1] FALSE
D29V7, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   9
  ZNF598 WILD-TYPE 227 425
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    9
  ZNF598 WILD-TYPE  227  425
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              2              227
  MALE                9              425
[1] 2 2
[1] FALSE
D29V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZNF598 MUTATED                    1                                 0
  ZNF598 WILD-TYPE                 65                               436
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZNF598 MUTATED                                      10
  ZNF598 WILD-TYPE                                   151
D29V9, multiclass
                                       clus
vv                                      ZNF598 MUTATED ZNF598 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  0              436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             10              151
[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, continuous
D29V11, continuous
[1] "Remove cluster labels:" "ZNF598 MUTATED"        
clus
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               1               31 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-G7-6795       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF598 MUTATED                                  0     0
  ZNF598 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF598 MUTATED                           3     8
  ZNF598 WILD-TYPE                        63   557
D29V12, multiclass
                                  clus
vv                                 ZNF598 MUTATED ZNF598 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     3               63
  WHITE                                         8              557
[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"
D29V13, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     1   9
  ZNF598 WILD-TYPE  30 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      1    9
  ZNF598 WILD-TYPE   30  432
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  1               30
  NOT HISPANIC OR LATINO              9              432
[1] 2 2
[1] FALSE

Clustering(30) Variable = KDM6A MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     5   3
  KDM6A WILD-TYPE 471 180
  KDM6A MUTATED KDM6A WILD-TYPE 
              8             651 
  KDM6A MUTATED KDM6A WILD-TYPE 
              3             180 
$`KDM6A MUTATED`
TCGA-B0-5075 TCGA-B2-4098 TCGA-CZ-5465 TCGA-A4-7584 TCGA-A4-A48D TCGA-BQ-5886 
       20.94         1.68        84.30        21.37        12.46        26.04 
TCGA-BQ-7060 TCGA-IZ-A6M8 
        7.04        16.34 

$`KDM6A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5077 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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
       35.90        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  KDM6A MUTATED KDM6A WILD-TYPE 
           1.68            0.07 
  KDM6A MUTATED KDM6A WILD-TYPE 
          84.30          194.79 
  KDM6A MUTATED KDM6A WILD-TYPE 
          18.64           37.58 
[1] "1.7 - 84.3 (18.6)"  "0.1 - 194.8 (37.6)"
[1] "hr=" "2.5"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         6        0         4        0
  KDM6A WILD-TYPE     319       76       159       88
D30V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               6             319
  STAGE II              0              76
  STAGE III             4             159
  STAGE IV              0              88
[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
  KDM6A MUTATED     5   1   4   0
  KDM6A WILD-TYPE 332  94 217  10
D30V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             5             332
  T2             1              94
  T3             4             217
  T4             0              10
[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               N0  N1  N2
  KDM6A MUTATED     1   0   0
  KDM6A WILD-TYPE 271  35   6
D30V5, multiclass
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317      TCGA-A3-3331 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3450 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5092 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691      TCGA-B0-5692 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5697 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713      TCGA-B2-5633 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4621 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159      TCGA-B8-5163 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545      TCGA-B8-5546 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5553 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160      TCGA-BP-4162 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331      TCGA-BP-4337 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342      TCGA-BP-4343 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351      TCGA-BP-4352 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761      TCGA-BP-4768 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787      TCGA-BP-4795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799      TCGA-BP-4960 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4986 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995      TCGA-BP-5006 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198      TCGA-BP-5199 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638      TCGA-CJ-4639 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891      TCGA-CJ-4892 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904      TCGA-CJ-4918 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033      TCGA-CW-5585 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4856 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-5451 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456      TCGA-CZ-5467 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984      TCGA-CZ-5985 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-A4-7583 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A5Y1 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656      TCGA-B1-A657 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
D30V6, binary
                 cls
clus                0   1
  KDM6A MUTATED     7   0
  KDM6A WILD-TYPE 456  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      7    0
  KDM6A WILD-TYPE  456   78
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             7             456
  1             0              78
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     4   6
  KDM6A WILD-TYPE 225 428
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4    6
  KDM6A WILD-TYPE  225  428
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4             225
  MALE               6             428
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              91 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5469 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KDM6A MUTATED                    0                                 3
  KDM6A WILD-TYPE                 66                               433
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KDM6A MUTATED                                       7
  KDM6A WILD-TYPE                                   154
D30V9, multiclass
                                       clus
vv                                      KDM6A MUTATED KDM6A WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             7             154
[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, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              49 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A57E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-IA-A40U      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" 
D30V11, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              31 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  1     0
  KDM6A WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           4     2
  KDM6A WILD-TYPE                        62   563
D30V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    4              62
  WHITE                                        2             563
[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"
D30V13, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   6
  KDM6A WILD-TYPE  31 435
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    6
  KDM6A WILD-TYPE   31  435
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             6             435
[1] 2 2
[1] FALSE

Clustering(31) Variable = DPCR1 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED     5   3
  DPCR1 WILD-TYPE 471 180
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             651 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              3             180 
$`DPCR1 MUTATED`
TCGA-KN-8435 TCGA-B0-5080 TCGA-CW-5589 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 
      115.00        11.24        78.18        61.41        94.45         1.94 
TCGA-DV-5576 TCGA-GL-A59R 
       23.90        12.43 

$`DPCR1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       66.31        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-5451 TCGA-CZ-5452 
       14.66       107.54        63.39         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        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        13.28        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
       12.16        11.67        66.28        56.84        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
        1.05        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           1.94            0.07 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         115.00          194.79 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         42.655          37.380 
[1] "1.9 - 115.0 (42.7)" "0.1 - 194.8 (37.4)"
[1] "hr=" "1.3"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DPCR1 MUTATED         3        1         1        3
  DPCR1 WILD-TYPE     322       75       162       85
D31V3, multiclass
           clus
vv          DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I               3             322
  STAGE II              1              75
  STAGE III             1             162
  STAGE IV              3              85
[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   1   4   0
  DPCR1 WILD-TYPE 334  94 217  10
D31V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             3             334
  T2             1              94
  T3             4             217
  T4             0              10
[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               N0  N1  N2
  DPCR1 MUTATED     2   0   0
  DPCR1 WILD-TYPE 270  35   6
D31V5, multiclass
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              2             311 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317      TCGA-A3-3331 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3450 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5081      TCGA-B0-5083 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5092 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691      TCGA-B0-5692 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696      TCGA-B0-5697 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713      TCGA-B2-5633 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4621 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159      TCGA-B8-5163 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545      TCGA-B8-5546 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5553 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160      TCGA-BP-4162 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331      TCGA-BP-4337 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342      TCGA-BP-4343 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351      TCGA-BP-4352 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761      TCGA-BP-4768 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787      TCGA-BP-4795 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799      TCGA-BP-4960 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4986 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995      TCGA-BP-5006 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198      TCGA-BP-5199 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638      TCGA-CJ-4639 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891      TCGA-CJ-4892 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904      TCGA-CJ-4918 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033      TCGA-CW-5585 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4856 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-5451 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456      TCGA-CZ-5467 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984      TCGA-CZ-5985 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-A4-7583 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A5Y1 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656      TCGA-B1-A657 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
D31V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 460  75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      3    3
  DPCR1 WILD-TYPE  460   75
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             3             460
  1             3              75
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     2   6
  DPCR1 WILD-TYPE 227 428
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      2    6
  DPCR1 WILD-TYPE  227  428
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             2             227
  MALE               6             428
[1] 2 2
[1] FALSE
D31V8, continuous
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              92 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  DPCR1 MUTATED                    1                                 6
  DPCR1 WILD-TYPE                 65                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DPCR1 MUTATED                                       1
  DPCR1 WILD-TYPE                                   160
D31V9, multiclass
                                       clus
vv                                      DPCR1 MUTATED DPCR1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[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"
D31V10, continuous
D31V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPCR1 MUTATED                                  0     0
  DPCR1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED                           1     7
  DPCR1 WILD-TYPE                        65   558
D31V12, multiclass
                                  clus
vv                                 DPCR1 MUTATED DPCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              65
  WHITE                                        7             558
[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"
D31V13, binary
                 cls
clus                0   1
  DPCR1 MUTATED     0   8
  DPCR1 WILD-TYPE  31 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      0    8
  DPCR1 WILD-TYPE   31  433
                        clus
vv                       DPCR1 MUTATED DPCR1 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             8             433
[1] 2 2
[1] FALSE

Clustering(32) Variable = CYP4F11 MUTATION ANALYSIS
D32V1, survival
                   sevent
clus2                 0   1
  CYP4F11 MUTATED     4   1
  CYP4F11 WILD-TYPE 472 182
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               654 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                1               182 
$`CYP4F11 MUTATED`
TCGA-KN-8427 TCGA-AK-3428 TCGA-B4-5844 TCGA-BP-4338 TCGA-BP-4787 
        0.99        73.08         0.23        93.99        15.78 

$`CYP4F11 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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-4340 TCGA-BP-4341 TCGA-BP-4342 
       62.07        80.68         0.07        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-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       68.38        11.64        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 
        6.90        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 
        1.74        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       115.00        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       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        10.72        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
      115.69        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 
      109.84        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
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 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
             0.23              0.07 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
            93.99            194.79 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
            15.78             37.43 
[1] "0.2 - 94.0 (15.8)"  "0.1 - 194.8 (37.4)"
[1] "hr=" "1.1"
D32V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CYP4F11 MUTATED         1        1         1        2
  CYP4F11 WILD-TYPE     324       75       162       86
D32V3, multiclass
           clus
vv          CYP4F11 MUTATED CYP4F11 WILD-TYPE
  STAGE I                 1               324
  STAGE II                1                75
  STAGE III               1               162
  STAGE IV                2                86
[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
  CYP4F11 MUTATED     1   1   2   1
  CYP4F11 WILD-TYPE 336  94 219   9
D32V4, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  T1               1               336
  T2               1                94
  T3               2               219
  T4               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP4F11 MUTATED     4   1   0
  CYP4F11 WILD-TYPE 268  34   6
D32V5, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  N0               4               268
  N1               1                34
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   1
  CYP4F11 WILD-TYPE 460  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    1
  CYP4F11 WILD-TYPE  460   77
   clus
vv  CYP4F11 MUTATED CYP4F11 WILD-TYPE
  0               3               460
  1               1                77
[1] 2 2
[1] FALSE
D32V7, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     2   3
  CYP4F11 WILD-TYPE 227 431
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      2    3
  CYP4F11 WILD-TYPE  227  431
        clus
vv       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  FEMALE               2               227
  MALE                 3               431
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "CYP4F11 MUTATED"       
clus
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                1                92 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8411 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-KO-8413        TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B8-4143        TCGA-B8-4622 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5568 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-IA-A40U 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CYP4F11 MUTATED                    1                                 4
  CYP4F11 WILD-TYPE                 65                               432
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CYP4F11 MUTATED                                       0
  CYP4F11 WILD-TYPE                                   161
D32V9, multiclass
                                       clus
vv                                      CYP4F11 MUTATED CYP4F11 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   4               432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               0               161
[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"
D32V10, continuous
D32V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4F11 MUTATED                                  0     0
  CYP4F11 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4F11 MUTATED                           0     5
  CYP4F11 WILD-TYPE                        66   560
D32V12, multiclass
                                  clus
vv                                 CYP4F11 MUTATED CYP4F11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      0                66
  WHITE                                          5               560
[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"
D32V13, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     0   2
  CYP4F11 WILD-TYPE  31 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      0    2
  CYP4F11 WILD-TYPE   31  439
                        clus
vv                       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  HISPANIC OR LATINO                   0                31
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(33) Variable = STAM MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  STAM MUTATED     4   2
  STAM WILD-TYPE 472 181
  STAM MUTATED STAM WILD-TYPE 
             6            653 
  STAM MUTATED STAM WILD-TYPE 
             2            181 
$`STAM MUTATED`
TCGA-KN-8435 TCGA-KO-8404 TCGA-BP-5200 TCGA-CJ-4639 TCGA-BQ-5889 TCGA-BQ-5894 
      115.00        10.68        34.95       106.16        10.82         2.76 

$`STAM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        31.27         0.95       115.00        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       63.25        73.22        14.17       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        13.25         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  STAM MUTATED STAM WILD-TYPE 
          2.76           0.07 
  STAM MUTATED STAM WILD-TYPE 
        115.00         194.79 
  STAM MUTATED STAM WILD-TYPE 
        22.885         37.480 
[1] "2.8 - 115.0 (22.9)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1.3"
D33V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  STAM MUTATED         0        3         0        3
  STAM WILD-TYPE     325       73       163       85
D33V3, multiclass
           clus
vv          STAM MUTATED STAM WILD-TYPE
  STAGE I              0            325
  STAGE II             3             73
  STAGE III            0            163
  STAGE IV             3             85
[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
  STAM MUTATED     0   3   2   1
  STAM WILD-TYPE 337  92 219   9
D33V4, multiclass
    clus
vv   STAM MUTATED STAM WILD-TYPE
  T1            0            337
  T2            3             92
  T3            2            219
  T4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  STAM MUTATED     1   2   0
  STAM WILD-TYPE 271  33   6
D33V5, multiclass
    clus
vv   STAM MUTATED STAM WILD-TYPE
  N0            1            271
  N1            2             33
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                cls
clus               0   1
  STAM MUTATED     2   2
  STAM WILD-TYPE 461  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      2    2
  STAM WILD-TYPE  461   76
   clus
vv  STAM MUTATED STAM WILD-TYPE
  0            2            461
  1            2             76
[1] 2 2
[1] FALSE
D33V7, binary
                cls
clus               0   1
  STAM MUTATED     1   5
  STAM WILD-TYPE 228 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      1    5
  STAM WILD-TYPE  228  429
        clus
vv       STAM MUTATED STAM WILD-TYPE
  FEMALE            1            228
  MALE              5            429
[1] 2 2
[1] FALSE
D33V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  STAM MUTATED                    2                                 2
  STAM WILD-TYPE                 64                               434
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  STAM MUTATED                                       2
  STAM WILD-TYPE                                   159
D33V9, multiclass
                                       clus
vv                                      STAM MUTATED STAM WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                2            434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[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"
D33V10, continuous
D33V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAM MUTATED                                  0     0
  STAM WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STAM MUTATED                           0     5
  STAM WILD-TYPE                        66   560
D33V12, multiclass
                                  clus
vv                                 STAM MUTATED STAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             66
  WHITE                                       5            560
[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"
D33V13, binary
                cls
clus               0   1
  STAM MUTATED     2   3
  STAM WILD-TYPE  29 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      2    3
  STAM WILD-TYPE   29  438
                        clus
vv                       STAM MUTATED STAM WILD-TYPE
  HISPANIC OR LATINO                2             29
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(34) Variable = NUDT11 MUTATION ANALYSIS
D34V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     5   0
  NUDT11 WILD-TYPE 471 183
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              654 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               0              183 
$`NUDT11 MUTATED`
TCGA-B4-5838 TCGA-B8-4153 TCGA-BP-5195 TCGA-BP-5202 TCGA-DW-7839 
        5.46        25.05        24.62         0.95        13.78 

$`NUDT11 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       42.71        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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-5196 TCGA-BP-5198 
       33.24        31.79        23.47        13.41        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       44.55        34.95        31.27       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 
       48.85        13.61       129.86        37.55        24.46         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            0.95             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           25.05           194.79 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
          13.780           37.565 
[1] "0.9 - 25.1 (13.8)"  "0.1 - 194.8 (37.6)"
[1] "hr="     "1200000"
D34V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NUDT11 MUTATED         2        0         2        1
  NUDT11 WILD-TYPE     323       76       161       87
D34V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                2              323
  STAGE II               0               76
  STAGE III              2              161
  STAGE IV               1               87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  NUDT11 MUTATED     2   0   3   0
  NUDT11 WILD-TYPE 335  95 218  10
D34V4, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T1              2              335
  T2              0               95
  T3              3              218
  T4              0               10
[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                N0  N1  N2
  NUDT11 MUTATED     0   1   0
  NUDT11 WILD-TYPE 272  34   6
D34V5, multiclass
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              312 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3313       TCGA-A3-3317       TCGA-A3-3331 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5843 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4621 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159       TCGA-B8-5163 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545       TCGA-B8-5546 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5553 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160       TCGA-BP-4162 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331       TCGA-BP-4337 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342       TCGA-BP-4343 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351       TCGA-BP-4352 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761       TCGA-BP-4768 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787       TCGA-BP-4795 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799       TCGA-BP-4960 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4986 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995       TCGA-BP-5006 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198       TCGA-BP-5199 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638       TCGA-CJ-4639 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891       TCGA-CJ-4892 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904       TCGA-CJ-4918 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033       TCGA-CW-5585 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4856 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A5Y1 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
D34V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     4   0
  NUDT11 WILD-TYPE 459  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      4    0
  NUDT11 WILD-TYPE  459   78
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              4              459
  1              0               78
[1] 2 2
[1] FALSE
D34V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     1   4
  NUDT11 WILD-TYPE 228 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      1    4
  NUDT11 WILD-TYPE  228  430
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              1              228
  MALE                4              430
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2               91 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854       TCGA-CZ-4856 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5456 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5568 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575       TCGA-DV-5576 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NUDT11 MUTATED                    0                                 4
  NUDT11 WILD-TYPE                 66                               432
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NUDT11 MUTATED                                       1
  NUDT11 WILD-TYPE                                   160
D34V9, multiclass
                                       clus
vv                                      NUDT11 MUTATED NUDT11 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              1              160
[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"
D34V10, continuous
D34V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           0     5
  NUDT11 WILD-TYPE                        66   560
D34V12, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     0               66
  WHITE                                         5              560
[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"
D34V13, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     0   4
  NUDT11 WILD-TYPE  31 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    4
  NUDT11 WILD-TYPE   31  437
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              4              437
[1] 2 2
[1] FALSE

Clustering(35) Variable = PARD6B MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  PARD6B MUTATED     4   1
  PARD6B WILD-TYPE 472 182
  PARD6B MUTATED PARD6B WILD-TYPE 
               5              654 
  PARD6B MUTATED PARD6B WILD-TYPE 
               1              182 
$`PARD6B MUTATED`
TCGA-B0-5694 TCGA-B0-5702 TCGA-A4-7584 TCGA-BQ-5886 TCGA-BQ-7044 
       15.78        71.41        21.37        26.04       123.62 

$`PARD6B WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
        7.66         0.95        11.97         7.92         2.76        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  PARD6B MUTATED PARD6B WILD-TYPE 
           15.78             0.07 
  PARD6B MUTATED PARD6B WILD-TYPE 
          123.62           194.79 
  PARD6B MUTATED PARD6B WILD-TYPE 
           26.04            37.43 
[1] "15.8 - 123.6 (26.0)" "0.1 - 194.8 (37.4)" 
[1] "hr=" "1.5"
D35V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PARD6B MUTATED         2        0         3        0
  PARD6B WILD-TYPE     323       76       160       88
D35V3, multiclass
           clus
vv          PARD6B MUTATED PARD6B WILD-TYPE
  STAGE I                2              323
  STAGE II               0               76
  STAGE III              3              160
  STAGE IV               0               88
[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
  PARD6B MUTATED     2   0   3   0
  PARD6B WILD-TYPE 335  95 218  10
D35V4, multiclass
    clus
vv   PARD6B MUTATED PARD6B WILD-TYPE
  T1              2              335
  T2              0               95
  T3              3              218
  T4              0               10
[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                N0  N1  N2
  PARD6B MUTATED     2   0   0
  PARD6B WILD-TYPE 270  35   6
D35V5, multiclass
[1] "Remove cluster labels:" "PARD6B MUTATED"        
clus
  PARD6B MUTATED PARD6B WILD-TYPE 
               2              311 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3313       TCGA-A3-3317       TCGA-A3-3331 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5695       TCGA-B0-5696       TCGA-B0-5697 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5703 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4621       TCGA-B8-4622 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5159       TCGA-B8-5163       TCGA-B8-5164 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-5165       TCGA-B8-5545       TCGA-B8-5546       TCGA-B8-5549 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5553       TCGA-BP-4158 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4159       TCGA-BP-4160       TCGA-BP-4162       TCGA-BP-4163 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4330       TCGA-BP-4331       TCGA-BP-4337       TCGA-BP-4338 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4340       TCGA-BP-4342       TCGA-BP-4343       TCGA-BP-4345 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4346       TCGA-BP-4351       TCGA-BP-4352       TCGA-BP-4354 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4756       TCGA-BP-4761       TCGA-BP-4768       TCGA-BP-4770 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4771       TCGA-BP-4787       TCGA-BP-4795       TCGA-BP-4797 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4798       TCGA-BP-4799       TCGA-BP-4960       TCGA-BP-4964 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4986       TCGA-BP-4988 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4989       TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5007 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-5191       TCGA-BP-5198       TCGA-BP-5199       TCGA-BP-5201 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4636       TCGA-CJ-4638       TCGA-CJ-4639       TCGA-CJ-4640 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874       TCGA-CJ-4876 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4890       TCGA-CJ-4891       TCGA-CJ-4892       TCGA-CJ-4894 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4900       TCGA-CJ-4904       TCGA-CJ-4918       TCGA-CJ-5678 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-6030       TCGA-CJ-6033       TCGA-CW-5585       TCGA-CW-5591 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4857 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451       TCGA-CZ-5452 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467       TCGA-CZ-5469 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985       TCGA-CZ-5986 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583       TCGA-A4-7585 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A5Y1       TCGA-AL-3466 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657       TCGA-B9-7268 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879       TCGA-BQ-5880 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058       TCGA-DW-7963 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966       TCGA-GL-A59R 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
D35V6, binary
                  cls
clus                 0   1
  PARD6B MUTATED     4   0
  PARD6B WILD-TYPE 459  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      4    0
  PARD6B WILD-TYPE  459   78
   clus
vv  PARD6B MUTATED PARD6B WILD-TYPE
  0              4              459
  1              0               78
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                 0   1
  PARD6B MUTATED     0   5
  PARD6B WILD-TYPE 229 429
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      0    5
  PARD6B WILD-TYPE  229  429
        clus
vv       PARD6B MUTATED PARD6B WILD-TYPE
  FEMALE              0              229
  MALE                5              429
[1] 2 2
[1] FALSE
D35V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PARD6B MUTATED                    0                                 2
  PARD6B WILD-TYPE                 66                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PARD6B MUTATED                                       3
  PARD6B WILD-TYPE                                   158
D35V9, multiclass
                                       clus
vv                                      PARD6B MUTATED PARD6B WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              158
[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"
D35V10, continuous
D35V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PARD6B MUTATED                                  0     0
  PARD6B WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PARD6B MUTATED                           1     4
  PARD6B WILD-TYPE                        65   561
D35V12, multiclass
                                  clus
vv                                 PARD6B MUTATED PARD6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               65
  WHITE                                         4              561
[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"
D35V13, binary
                  cls
clus                 0   1
  PARD6B MUTATED     0   3
  PARD6B WILD-TYPE  31 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      0    3
  PARD6B WILD-TYPE   31  438
                        clus
vv                       PARD6B MUTATED PARD6B WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              3              438
[1] 2 2
[1] FALSE

Clustering(36) Variable = RHEB MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  RHEB MUTATED     2   1
  RHEB WILD-TYPE 474 182
  RHEB MUTATED RHEB WILD-TYPE 
             3            656 
  RHEB MUTATED RHEB WILD-TYPE 
             1            182 
$`RHEB MUTATED`
TCGA-CJ-4895 TCGA-CJ-5686 TCGA-Q2-A5QZ 
       39.45        67.00        14.07 

$`RHEB WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       62.10        73.35       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       19.73        17.75 

  RHEB MUTATED RHEB WILD-TYPE 
         14.07           0.07 
  RHEB MUTATED RHEB WILD-TYPE 
         67.00         194.79 
  RHEB MUTATED RHEB WILD-TYPE 
        39.450         37.315 
[1] "14.1 - 67.0 (39.5)" "0.1 - 194.8 (37.3)"
[1] "hr=" "1.3"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHEB MUTATED         1        0         1        1
  RHEB WILD-TYPE     324       76       162       87
D36V3, multiclass
           clus
vv          RHEB MUTATED RHEB WILD-TYPE
  STAGE I              1            324
  STAGE II             0             76
  STAGE III            1            162
  STAGE IV             1             87
[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
  RHEB MUTATED     1   0   2   0
  RHEB WILD-TYPE 336  95 219  10
D36V4, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  T1            1            336
  T2            0             95
  T3            2            219
  T4            0             10
[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              N0  N1  N2
  RHEB MUTATED     0   0   0
  RHEB WILD-TYPE 272  35   6
D36V5, multiclass
D36V6, binary
                cls
clus               0   1
  RHEB MUTATED     1   1
  RHEB WILD-TYPE 462  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      1    1
  RHEB WILD-TYPE  462   77
   clus
vv  RHEB MUTATED RHEB WILD-TYPE
  0            1            462
  1            1             77
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus               0   1
  RHEB MUTATED     2   1
  RHEB WILD-TYPE 227 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      2    1
  RHEB WILD-TYPE  227  433
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  FEMALE            2            227
  MALE              1            433
[1] 2 2
[1] FALSE
D36V8, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             92 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8411 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KO-8413     TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4854 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RHEB MUTATED                    0                                 2
  RHEB WILD-TYPE                 66                               434
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RHEB MUTATED                                       1
  RHEB WILD-TYPE                                   160
D36V9, multiclass
                                       clus
vv                                      RHEB MUTATED RHEB WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                2            434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[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"
D36V10, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             50 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-4621     TCGA-B8-5158 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5550     TCGA-A4-8310     TCGA-A4-A48D 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A44B     TCGA-B9-A69E 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838     TCGA-DW-7963 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A59T     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IZ-A6M8     TCGA-P4-A5E7 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-P4-A5EB     TCGA-PJ-A5Z9 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" 
D36V11, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             31 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-7773     TCGA-HE-A5NI 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHEB MUTATED                                  0     0
  RHEB WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHEB MUTATED                           1     2
  RHEB WILD-TYPE                        65   563
D36V12, multiclass
                                  clus
vv                                 RHEB MUTATED RHEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             65
  WHITE                                       2            563
[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"
D36V13, binary
                cls
clus               0   1
  RHEB MUTATED     0   3
  RHEB WILD-TYPE  31 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      0    3
  RHEB WILD-TYPE   31  438
                        clus
vv                       RHEB MUTATED RHEB WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(37) Variable = SLC16A1 MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     3   0
  SLC16A1 WILD-TYPE 473 183
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               656 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                0               183 
$`SLC16A1 MUTATED`
TCGA-B4-5834 TCGA-CJ-5676 TCGA-B3-8121 
        0.85       133.71        12.46 

$`SLC16A1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5836 
       24.82        21.57        12.00         5.10         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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         1.74        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 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        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-5677 
        4.57        18.81       131.08        72.00       129.40        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       33.83        10.09        30.58        34.49        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             0.85              0.07 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           133.71            194.79 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
            12.46             37.43 
[1] "0.8 - 133.7 (12.5)" "0.1 - 194.8 (37.4)"
[1] "hr="     "1200000"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC16A1 MUTATED         2        0         1        0
  SLC16A1 WILD-TYPE     323       76       162       88
D37V3, multiclass
           clus
vv          SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                 2               323
  STAGE II                0                76
  STAGE III               1               162
  STAGE IV                0                88
[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
  SLC16A1 MUTATED     2   0   1   0
  SLC16A1 WILD-TYPE 335  95 220  10
D37V4, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               2               335
  T2               0                95
  T3               1               220
  T4               0                10
[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                 N0  N1  N2
  SLC16A1 MUTATED     1   0   0
  SLC16A1 WILD-TYPE 271  35   6
D37V5, multiclass
[1] "Remove cluster labels:" "SLC16A1 MUTATED"       
clus
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1               312 
       TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328        TCGA-KL-8329 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332        TCGA-KL-8333 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336        TCGA-KL-8337 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340        TCGA-KL-8341 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8430        TCGA-KO-8405        TCGA-KO-8406 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8410 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8413        TCGA-KO-8414        TCGA-KO-8415        TCGA-KO-8416 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8417        TCGA-A3-3313        TCGA-A3-3317        TCGA-A3-3331 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3347        TCGA-A3-3349        TCGA-A3-3357        TCGA-A3-3358 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3362        TCGA-A3-3367        TCGA-A3-3370        TCGA-A3-3373 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3374        TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3427        TCGA-AK-3428        TCGA-AK-3429 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AK-3430        TCGA-AK-3436        TCGA-AK-3443        TCGA-AK-3450 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AK-3451        TCGA-AK-3456        TCGA-B0-4690        TCGA-B0-4691 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4693        TCGA-B0-4703        TCGA-B0-4710        TCGA-B0-4810 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4811        TCGA-B0-4814        TCGA-B0-4816        TCGA-B0-4817 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4823        TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4833 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4838        TCGA-B0-4839        TCGA-B0-4842 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4843        TCGA-B0-4846        TCGA-B0-4852        TCGA-B0-4945 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5075        TCGA-B0-5077        TCGA-B0-5080        TCGA-B0-5081 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5083        TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5092        TCGA-B0-5094        TCGA-B0-5095        TCGA-B0-5096 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5097        TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110        TCGA-B0-5113 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119        TCGA-B0-5120 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5691 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5707        TCGA-B0-5710        TCGA-B0-5712        TCGA-B0-5713 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5832 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-B8-4621 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159        TCGA-B8-5163 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545        TCGA-B8-5546 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5553 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4158        TCGA-BP-4159        TCGA-BP-4160        TCGA-BP-4162 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4165        TCGA-BP-4166        TCGA-BP-4169 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4170        TCGA-BP-4173        TCGA-BP-4174        TCGA-BP-4326 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4329        TCGA-BP-4330        TCGA-BP-4331        TCGA-BP-4337 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4338        TCGA-BP-4340        TCGA-BP-4342        TCGA-BP-4343 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4345        TCGA-BP-4346        TCGA-BP-4351        TCGA-BP-4352 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4354        TCGA-BP-4756        TCGA-BP-4761        TCGA-BP-4768 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4770        TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4795 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4798        TCGA-BP-4799        TCGA-BP-4960 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4964        TCGA-BP-4967        TCGA-BP-4968        TCGA-BP-4970 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4971        TCGA-BP-4974        TCGA-BP-4985        TCGA-BP-4986 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4995        TCGA-BP-5006 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5010        TCGA-BP-5169        TCGA-BP-5182 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5186        TCGA-BP-5191        TCGA-BP-5198        TCGA-BP-5199 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5201        TCGA-CJ-4636        TCGA-CJ-4638        TCGA-CJ-4639 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4643        TCGA-CJ-4644        TCGA-CJ-4868 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4869        TCGA-CJ-4872        TCGA-CJ-4873        TCGA-CJ-4874 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4892 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4894        TCGA-CJ-4900        TCGA-CJ-4904        TCGA-CJ-4918 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-5678        TCGA-CJ-6030        TCGA-CJ-6033        TCGA-CW-5585 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CW-5591        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4856 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-5451 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5454        TCGA-CZ-5456        TCGA-CZ-5467 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5984        TCGA-CZ-5985 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5986        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-A4-7583 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E        TCGA-A4-A5Y1 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656        TCGA-B1-A657 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7058 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846        TCGA-GL-7966 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-J7-8537        TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
D37V6, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     2   0
  SLC16A1 WILD-TYPE 461  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      2    0
  SLC16A1 WILD-TYPE  461   78
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               2               461
  1               0                78
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     1   2
  SLC16A1 WILD-TYPE 228 432
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      1    2
  SLC16A1 WILD-TYPE  228  432
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               1               228
  MALE                 2               432
[1] 2 2
[1] FALSE
D37V8, continuous
[1] "Remove cluster labels:" "SLC16A1 MUTATED"       
clus
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1                92 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8411 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8413        TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5568 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-IA-A40U 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC16A1 MUTATED                    0                                 2
  SLC16A1 WILD-TYPE                 66                               434
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC16A1 MUTATED                                       1
  SLC16A1 WILD-TYPE                                   160
D37V9, multiclass
                                       clus
vv                                      SLC16A1 MUTATED SLC16A1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               160
[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"
D37V10, continuous
D37V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A1 MUTATED                                  0     0
  SLC16A1 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A1 MUTATED                           1     2
  SLC16A1 WILD-TYPE                        65   563
D37V12, multiclass
                                  clus
vv                                 SLC16A1 MUTATED SLC16A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                65
  WHITE                                          2               563
[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"
D37V13, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     1   2
  SLC16A1 WILD-TYPE  30 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      1    2
  SLC16A1 WILD-TYPE   30  439
                        clus
vv                       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  HISPANIC OR LATINO                   1                30
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(38) Variable = SKI MUTATION ANALYSIS
D38V1, survival
               sevent
clus2             0   1
  SKI MUTATED     7   2
  SKI WILD-TYPE 469 181
  SKI MUTATED SKI WILD-TYPE 
            9           650 
  SKI MUTATED SKI WILD-TYPE 
            2           181 
$`SKI MUTATED`
TCGA-KL-8330 TCGA-KO-8408 TCGA-AS-3777 TCGA-A4-7585 TCGA-B9-7268 TCGA-BQ-5884 
      108.62        16.67        40.70        35.18        22.06        26.04 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
       80.88        61.02        74.60 

$`SKI WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71       104.55       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       12.13         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        21.37        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       20.61         0.46        43.99         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 
       22.92        43.20        47.80        21.63        40.83        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 
        3.02        40.77        79.86        51.19        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  SKI MUTATED SKI WILD-TYPE 
        16.67          0.07 
  SKI MUTATED SKI WILD-TYPE 
       108.62        194.79 
  SKI MUTATED SKI WILD-TYPE 
       40.700        37.315 
[1] "16.7 - 108.6 (40.7)" "0.1 - 194.8 (37.3)" 
[1] "hr=" "1.5"
D38V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SKI MUTATED         5        2         2        0
  SKI WILD-TYPE     320       74       161       88
D38V3, multiclass
           clus
vv          SKI MUTATED SKI WILD-TYPE
  STAGE I             5           320
  STAGE II            2            74
  STAGE III           2           161
  STAGE IV            0            88
[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
  SKI MUTATED     5   2   2   0
  SKI WILD-TYPE 332  93 219  10
D38V4, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  T1           5           332
  T2           2            93
  T3           2           219
  T4           0            10
[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             N0  N1  N2
  SKI MUTATED     3   1   0
  SKI WILD-TYPE 269  34   6
D38V5, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  N0           3           269
  N1           1            34
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
               cls
clus              0   1
  SKI MUTATED     5   0
  SKI WILD-TYPE 458  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      5    0
  SKI WILD-TYPE  458   78
   clus
vv  SKI MUTATED SKI WILD-TYPE
  0           5           458
  1           0            78
[1] 2 2
[1] FALSE
D38V7, binary
               cls
clus              0   1
  SKI MUTATED     2   7
  SKI WILD-TYPE 227 427
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      2    7
  SKI WILD-TYPE  227  427
        clus
vv       SKI MUTATED SKI WILD-TYPE
  FEMALE           2           227
  MALE             7           427
[1] 2 2
[1] FALSE
D38V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SKI MUTATED                    2                                 1
  SKI WILD-TYPE                 64                               435
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SKI MUTATED                                       6
  SKI WILD-TYPE                                   155
D38V9, multiclass
                                       clus
vv                                      SKI MUTATED SKI WILD-TYPE
  KIDNEY CHROMOPHOBE                              2            64
  KIDNEY CLEAR CELL RENAL CARCINOMA               1           435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           6           155
[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"
D38V10, continuous
D38V11, continuous
[1] "Remove cluster labels:" "SKI MUTATED"           
clus
  SKI MUTATED SKI WILD-TYPE 
            2            30 
   TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8433 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-KO-8409    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-5158    TCGA-B8-5550 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3472    TCGA-AL-7173 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4117    TCGA-B9-A69E    TCGA-DW-5561 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-DW-7963    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-GL-7773 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKI MUTATED                                  0     0
  SKI WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SKI MUTATED                           2     5
  SKI WILD-TYPE                        64   560
D38V12, multiclass
                                  clus
vv                                 SKI MUTATED SKI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  2            64
  WHITE                                      5           560
[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"
D38V13, binary
               cls
clus              0   1
  SKI MUTATED     0   5
  SKI WILD-TYPE  31 436
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      0    5
  SKI WILD-TYPE   31  436
                        clus
vv                       SKI MUTATED SKI WILD-TYPE
  HISPANIC OR LATINO               0            31
  NOT HISPANIC OR LATINO           5           436
[1] 2 2
[1] FALSE

Clustering(39) Variable = THBS1 MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  THBS1 MUTATED     8   2
  THBS1 WILD-TYPE 468 181
  THBS1 MUTATED THBS1 WILD-TYPE 
             10             649 
  THBS1 MUTATED THBS1 WILD-TYPE 
              2             181 
$`THBS1 MUTATED`
TCGA-B0-5099 TCGA-BP-4807 TCGA-BP-4977 TCGA-BP-5187 TCGA-CZ-5457 TCGA-CZ-5459 
       15.95         6.94        14.93        13.35        90.54        55.33 
TCGA-A4-A48D TCGA-B1-A656 TCGA-DZ-6133 TCGA-IZ-8195 
       12.46        20.32        51.19        22.26 

$`THBS1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-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         6.90        47.11        53.65 
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         1.74        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-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        37.22        22.78        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5460 
       79.53        23.74        18.44        79.63        91.69        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.28        23.31        19.63        19.73        14.33        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
       19.56        21.67        24.56        20.25        16.77        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23        17.23         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 
       25.22        16.80        19.99         2.04        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  THBS1 MUTATED THBS1 WILD-TYPE 
           6.94            0.07 
  THBS1 MUTATED THBS1 WILD-TYPE 
          90.54          194.79 
  THBS1 MUTATED THBS1 WILD-TYPE 
         18.135          37.550 
[1] "6.9 - 90.5 (18.1)"  "0.1 - 194.8 (37.5)"
[1] "hr=" "1"  
D39V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  THBS1 MUTATED         6        1         3        0
  THBS1 WILD-TYPE     319       75       160       88
D39V3, multiclass
           clus
vv          THBS1 MUTATED THBS1 WILD-TYPE
  STAGE I               6             319
  STAGE II              1              75
  STAGE III             3             160
  STAGE IV              0              88
[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
  THBS1 MUTATED     6   1   3   0
  THBS1 WILD-TYPE 331  94 218  10
D39V4, multiclass
    clus
vv   THBS1 MUTATED THBS1 WILD-TYPE
  T1             6             331
  T2             1              94
  T3             3             218
  T4             0              10
[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               N0  N1  N2
  THBS1 MUTATED     1   0   0
  THBS1 WILD-TYPE 271  35   6
D39V5, multiclass
[1] "Remove cluster labels:" "THBS1 MUTATED"         
clus
  THBS1 MUTATED THBS1 WILD-TYPE 
              1             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317      TCGA-A3-3331 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3450 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A657 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
D39V6, binary
                 cls
clus                0   1
  THBS1 MUTATED     7   0
  THBS1 WILD-TYPE 456  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      7    0
  THBS1 WILD-TYPE  456   78
   clus
vv  THBS1 MUTATED THBS1 WILD-TYPE
  0             7             456
  1             0              78
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus                0   1
  THBS1 MUTATED     2   8
  THBS1 WILD-TYPE 227 426
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      2    8
  THBS1 WILD-TYPE  227  426
        clus
vv       THBS1 MUTATED THBS1 WILD-TYPE
  FEMALE             2             227
  MALE               8             426
[1] 2 2
[1] FALSE
D39V8, continuous
[1] "Remove cluster labels:" "THBS1 MUTATED"         
clus
  THBS1 MUTATED THBS1 WILD-TYPE 
              2              91 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  THBS1 MUTATED                    0                                 6
  THBS1 WILD-TYPE                 66                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  THBS1 MUTATED                                       4
  THBS1 WILD-TYPE                                   157
D39V9, multiclass
                                       clus
vv                                      THBS1 MUTATED THBS1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             4             157
[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"
D39V10, continuous
[1] "Remove cluster labels:" "THBS1 MUTATED"         
clus
  THBS1 MUTATED THBS1 WILD-TYPE 
              1              50 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A57E 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
D39V11, continuous
[1] "Remove cluster labels:" "THBS1 MUTATED"         
clus
  THBS1 MUTATED THBS1 WILD-TYPE 
              1              31 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"THBS1 WILD-TYPE" "THBS1 WILD-TYPE" "THBS1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  THBS1 MUTATED                                  0     0
  THBS1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  THBS1 MUTATED                           1     9
  THBS1 WILD-TYPE                        65   556
D39V12, multiclass
                                  clus
vv                                 THBS1 MUTATED THBS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              65
  WHITE                                        9             556
[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"
D39V13, binary
                 cls
clus                0   1
  THBS1 MUTATED     0   5
  THBS1 WILD-TYPE  31 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  THBS1 MUTATED      0    5
  THBS1 WILD-TYPE   31  436
                        clus
vv                       THBS1 MUTATED THBS1 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(40) Variable = SH3BP2 MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  SH3BP2 MUTATED     4   0
  SH3BP2 WILD-TYPE 472 183
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              655 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               0              183 
$`SH3BP2 MUTATED`
TCGA-B4-5836 TCGA-A4-8311 TCGA-B9-4114 TCGA-BQ-5891 
        4.64        23.97        28.18         0.95 

$`SH3BP2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         0.53 
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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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         1.74        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 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-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       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        29.46        25.64        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       48.85        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       71.44        25.15        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       84.89        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
            0.95             0.07 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
           28.18           194.79 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
          14.305           37.550 
[1] "0.9 - 28.2 (14.3)"  "0.1 - 194.8 (37.5)"
[1] "hr="     "1200000"
D40V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SH3BP2 MUTATED         2        0         1        0
  SH3BP2 WILD-TYPE     323       76       162       88
D40V3, multiclass
           clus
vv          SH3BP2 MUTATED SH3BP2 WILD-TYPE
  STAGE I                2              323
  STAGE II               0               76
  STAGE III              1              162
  STAGE IV               0               88
[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
  SH3BP2 MUTATED     2   1   1   0
  SH3BP2 WILD-TYPE 335  94 220  10
D40V4, multiclass
    clus
vv   SH3BP2 MUTATED SH3BP2 WILD-TYPE
  T1              2              335
  T2              1               94
  T3              1              220
  T4              0               10
[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                N0  N1  N2
  SH3BP2 MUTATED     2   0   0
  SH3BP2 WILD-TYPE 270  35   6
D40V5, multiclass
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               2              311 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3313       TCGA-A3-3317       TCGA-A3-3331 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5838       TCGA-B4-5843 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4621 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159       TCGA-B8-5163 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545       TCGA-B8-5546 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5553 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160       TCGA-BP-4162 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331       TCGA-BP-4337 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342       TCGA-BP-4343 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351       TCGA-BP-4352 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761       TCGA-BP-4768 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787       TCGA-BP-4795 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799       TCGA-BP-4960 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4986 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995       TCGA-BP-5006 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198       TCGA-BP-5199 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638       TCGA-CJ-4639 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891       TCGA-CJ-4892 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904       TCGA-CJ-4918 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033       TCGA-CW-5585 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4856 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A5Y1 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5892 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058       TCGA-DW-7963 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966       TCGA-GL-A59R 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
D40V6, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     2   0
  SH3BP2 WILD-TYPE 461  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      2    0
  SH3BP2 WILD-TYPE  461   78
   clus
vv  SH3BP2 MUTATED SH3BP2 WILD-TYPE
  0              2              461
  1              0               78
[1] 2 2
[1] FALSE
D40V7, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     2   2
  SH3BP2 WILD-TYPE 227 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      2    2
  SH3BP2 WILD-TYPE  227  432
        clus
vv       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  FEMALE              2              227
  MALE                2              432
[1] 2 2
[1] FALSE
D40V8, continuous
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               2               91 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5838 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854       TCGA-CZ-4856 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5456 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5568 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575       TCGA-DV-5576 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-5560 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837       TCGA-DW-7838 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SH3BP2 MUTATED                    0                                 1
  SH3BP2 WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SH3BP2 MUTATED                                       3
  SH3BP2 WILD-TYPE                                   158
D40V9, multiclass
                                       clus
vv                                      SH3BP2 MUTATED SH3BP2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              158
[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"
D40V10, continuous
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               1               50 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A48D 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
D40V11, continuous
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               1               31 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4117       TCGA-B9-A69E 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793       TCGA-G7-6795 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SH3BP2 MUTATED                                  0     0
  SH3BP2 WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SH3BP2 MUTATED                           1     3
  SH3BP2 WILD-TYPE                        65   562
D40V12, multiclass
                                  clus
vv                                 SH3BP2 MUTATED SH3BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               65
  WHITE                                         3              562
[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"
D40V13, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     0   4
  SH3BP2 WILD-TYPE  31 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      0    4
  SH3BP2 WILD-TYPE   31  437
                        clus
vv                       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              4              437
[1] 2 2
[1] FALSE

Clustering(41) Variable = NASP MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  NASP MUTATED     2   2
  NASP WILD-TYPE 474 181
  NASP MUTATED NASP WILD-TYPE 
             4            655 
  NASP MUTATED NASP WILD-TYPE 
             2            181 
$`NASP MUTATED`
TCGA-KN-8433 TCGA-KO-8415 TCGA-CJ-5679 TCGA-P4-A5EA 
       11.21        96.62        22.32         6.61 

$`NASP WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
      105.60        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       87.09        42.94        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  NASP MUTATED NASP WILD-TYPE 
          6.61           0.07 
  NASP MUTATED NASP WILD-TYPE 
         96.62         194.79 
  NASP MUTATED NASP WILD-TYPE 
        16.765         37.480 
[1] "6.6 - 96.6 (16.8)"  "0.1 - 194.8 (37.5)"
[1] "hr=" "2.4"
D41V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NASP MUTATED         1        0         3        0
  NASP WILD-TYPE     324       76       160       88
D41V3, multiclass
           clus
vv          NASP MUTATED NASP WILD-TYPE
  STAGE I              1            324
  STAGE II             0             76
  STAGE III            3            160
  STAGE IV             0             88
[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
  NASP MUTATED     1   0   3   0
  NASP WILD-TYPE 336  95 218  10
D41V4, multiclass
    clus
vv   NASP MUTATED NASP WILD-TYPE
  T1            1            336
  T2            0             95
  T3            3            218
  T4            0             10
[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              N0  N1  N2
  NASP MUTATED     1   1   0
  NASP WILD-TYPE 271  34   6
D41V5, multiclass
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             2            311 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8416     TCGA-KO-8417 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3313     TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373     TCGA-A3-3374 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3376     TCGA-A3-3385     TCGA-A3-3387     TCGA-AK-3425 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429     TCGA-AK-3430 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3450     TCGA-AK-3451 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5092 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691     TCGA-B0-5692 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620     TCGA-B8-4621 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159     TCGA-B8-5163 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545     TCGA-B8-5546 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5553 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160     TCGA-BP-4162 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331     TCGA-BP-4337 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342     TCGA-BP-4343 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4795 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799     TCGA-BP-4960 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4986 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995     TCGA-BP-5006 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198     TCGA-BP-5199 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638     TCGA-CJ-4639 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891     TCGA-CJ-4892 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904     TCGA-CJ-4918 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033     TCGA-CW-5585 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4856 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
D41V6, binary
                cls
clus               0   1
  NASP MUTATED     2   0
  NASP WILD-TYPE 461  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      2    0
  NASP WILD-TYPE  461   78
   clus
vv  NASP MUTATED NASP WILD-TYPE
  0            2            461
  1            0             78
[1] 2 2
[1] FALSE
D41V7, binary
                cls
clus               0   1
  NASP MUTATED     3   1
  NASP WILD-TYPE 226 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      3    1
  NASP WILD-TYPE  226  433
        clus
vv       NASP MUTATED NASP WILD-TYPE
  FEMALE            3            226
  MALE              1            433
[1] 2 2
[1] FALSE
D41V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NASP MUTATED                    2                                 1
  NASP WILD-TYPE                 64                               435
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NASP MUTATED                                       1
  NASP WILD-TYPE                                   160
D41V9, multiclass
                                       clus
vv                                      NASP MUTATED NASP WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[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"
D41V10, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             50 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KO-8408 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445     TCGA-AK-3451 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-4621     TCGA-B8-5158     TCGA-B8-5164 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5550     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7838     TCGA-DW-7963     TCGA-G7-6792 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-7773 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-A59T     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" 
D41V11, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             31 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8408     TCGA-KO-8409     TCGA-AK-3445 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550     TCGA-A4-A48D 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NASP MUTATED                                  0     0
  NASP WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NASP MUTATED                           0     4
  NASP WILD-TYPE                        66   561
D41V12, multiclass
                                  clus
vv                                 NASP MUTATED NASP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   0             66
  WHITE                                       4            561
[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"
D41V13, binary
                cls
clus               0   1
  NASP MUTATED     1   3
  NASP WILD-TYPE  30 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      1    3
  NASP WILD-TYPE   30  438
                        clus
vv                       NASP MUTATED NASP WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(42) Variable = FAT1 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    15   6
  FAT1 WILD-TYPE 461 177
  FAT1 MUTATED FAT1 WILD-TYPE 
            21            638 
  FAT1 MUTATED FAT1 WILD-TYPE 
             6            177 
$`FAT1 MUTATED`
TCGA-KN-8436 TCGA-B0-5098 TCGA-B0-5713 TCGA-B8-4621 TCGA-B8-5550 TCGA-BP-4169 
       42.35        52.08        91.46        25.91        48.53        23.05 
TCGA-CJ-4641 TCGA-CZ-4859 TCGA-B1-A657 TCGA-B9-4116 TCGA-B9-7268 TCGA-B9-A69E 
       54.61        58.75        21.07        20.61        22.06        14.86 
TCGA-BQ-5877 TCGA-BQ-5885 TCGA-BQ-7061 TCGA-G7-6797 TCGA-GL-A59T TCGA-IZ-8195 
        8.88        30.28         7.17        25.15        17.95        22.26 
TCGA-J7-8537 TCGA-MH-A562 TCGA-P4-A5E8 
       10.55        20.25        42.94 

$`FAT1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        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        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
        6.38         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-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        89.36        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-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-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         6.90 
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         1.74 
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       115.00        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16       114.41        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        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-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-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       69.21        14.66       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       21.67        24.56        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       26.40         0.46        43.99         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        0.16        86.76        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       39.25        71.44        20.52        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NF 
       12.92         3.68        27.65         1.05        12.43        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
       19.99         2.04        21.34        16.34        12.36        12.76 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       99.78        87.09         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  FAT1 MUTATED FAT1 WILD-TYPE 
          7.17           0.07 
  FAT1 MUTATED FAT1 WILD-TYPE 
         91.46         194.79 
  FAT1 MUTATED FAT1 WILD-TYPE 
        23.050         37.825 
[1] "7.2 - 91.5 (23.1)"  "0.1 - 194.8 (37.8)"
[1] "hr=" "1.4"
D42V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         7        4         7        2
  FAT1 WILD-TYPE     318       72       156       86
D42V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              7            318
  STAGE II             4             72
  STAGE III            7            156
  STAGE IV             2             86
[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
  FAT1 MUTATED     8   6   7   0
  FAT1 WILD-TYPE 329  89 214  10
D42V4, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  T1            8            329
  T2            6             89
  T3            7            214
  T4            0             10
[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              N0  N1  N2
  FAT1 MUTATED     8   3   0
  FAT1 WILD-TYPE 264  32   6
D42V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0            8            264
  N1            3             32
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                cls
clus               0   1
  FAT1 MUTATED    12   2
  FAT1 WILD-TYPE 451  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     12    2
  FAT1 WILD-TYPE  451   76
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0           12            451
  1            2             76
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus               0   1
  FAT1 MUTATED     8  13
  FAT1 WILD-TYPE 221 421
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      8   13
  FAT1 WILD-TYPE  221  421
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE            8            221
  MALE             13            421
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "FAT1 MUTATED"          
clus
  FAT1 MUTATED FAT1 WILD-TYPE 
             2             91 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8411 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KO-8413     TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4854 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-Q2-A5QZ 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAT1 MUTATED                    1                                 7
  FAT1 WILD-TYPE                 65                               429
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAT1 MUTATED                                      13
  FAT1 WILD-TYPE                                   148
D42V9, multiclass
                                       clus
vv                                      FAT1 MUTATED FAT1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                7            429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           13            148
[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"
D42V10, continuous
D42V11, continuous
[1] "Remove cluster labels:" "FAT1 MUTATED"          
clus
  FAT1 MUTATED FAT1 WILD-TYPE 
             2             30 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-A4-A48D 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-DW-5561 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  0     1
  FAT1 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           5    15
  FAT1 WILD-TYPE                        61   550
D42V12, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   5             61
  WHITE                                      15            550
[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"
D42V13, binary
                cls
clus               0   1
  FAT1 MUTATED     0  18
  FAT1 WILD-TYPE  31 423
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      0   18
  FAT1 WILD-TYPE   31  423
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO           18            423
[1] 2 2
[1] FALSE

Clustering(43) Variable = CACNA1C MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  CACNA1C MUTATED    12   5
  CACNA1C WILD-TYPE 464 178
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               17               642 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
                5               178 
$`CACNA1C MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KL-8346 TCGA-A3-3331 TCGA-AK-3460 TCGA-B0-4844 
      137.06        28.11        62.37        48.82        82.45        10.29 
TCGA-B8-5163 TCGA-CJ-4638 TCGA-CJ-4869 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       27.02        14.17        83.97        90.54        94.45        10.85 
TCGA-A4-8310 TCGA-A4-8312 TCGA-B1-A47N TCGA-B9-4116 TCGA-BQ-5877 
       25.64        23.28        24.56        20.61         8.88 

$`CACNA1C WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        54.74       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      104.55       103.10       130.13        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       90.48        92.55        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 
       36.36        37.38        52.93        45.53        88.37        42.97 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91       117.80        73.08       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       78.64        49.28        94.29        83.21        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       37.58        38.40        72.89        12.13        40.70         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-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        10.52        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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       25.91        50.14        20.91        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-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         6.90        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         1.74        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-4639 TCGA-CJ-4640 
      115.00        46.55        63.25        73.22       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        11.05        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 
        0.23        16.64        30.48        29.46        23.97        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       17.23         0.16        14.86        86.76        19.27        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  CACNA1C MUTATED CACNA1C WILD-TYPE 
             8.88              0.07 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
           137.06            194.79 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
           27.020            37.515 
[1] "8.9 - 137.1 (27.0)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1"  
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CACNA1C MUTATED         5        1         4        6
  CACNA1C WILD-TYPE     320       75       159       82
D43V3, multiclass
           clus
vv          CACNA1C MUTATED CACNA1C WILD-TYPE
  STAGE I                 5               320
  STAGE II                1                75
  STAGE III               4               159
  STAGE IV                6                82
[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
  CACNA1C MUTATED     6   3   8   0
  CACNA1C WILD-TYPE 331  92 213  10
D43V4, multiclass
    clus
vv   CACNA1C MUTATED CACNA1C WILD-TYPE
  T1               6               331
  T2               3                92
  T3               8               213
  T4               0                10
[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                 N0  N1  N2
  CACNA1C MUTATED     4   4   0
  CACNA1C WILD-TYPE 268  31   6
D43V5, multiclass
    clus
vv   CACNA1C MUTATED CACNA1C WILD-TYPE
  N0               4               268
  N1               4                31
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  CACNA1C MUTATED     7   6
  CACNA1C WILD-TYPE 456  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      7    6
  CACNA1C WILD-TYPE  456   72
   clus
vv  CACNA1C MUTATED CACNA1C WILD-TYPE
  0               7               456
  1               6                72
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  CACNA1C MUTATED     5  12
  CACNA1C WILD-TYPE 224 422
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      5   12
  CACNA1C WILD-TYPE  224  422
        clus
vv       CACNA1C MUTATED CACNA1C WILD-TYPE
  FEMALE               5               224
  MALE                12               422
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CACNA1C MUTATED                    3                                 9
  CACNA1C WILD-TYPE                 63                               427
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CACNA1C MUTATED                                       5
  CACNA1C WILD-TYPE                                   156
D43V9, multiclass
                                       clus
vv                                      CACNA1C MUTATED CACNA1C WILD-TYPE
  KIDNEY CHROMOPHOBE                                  3                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                   9               427
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               5               156
[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"
D43V10, continuous
[1] "Remove cluster labels:" "CACNA1C MUTATED"       
clus
  CACNA1C MUTATED CACNA1C WILD-TYPE 
                1                50 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-AK-3451        TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-A4-A48D        TCGA-A4-A57E 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7838        TCGA-DW-7963        TCGA-G7-6792 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7773 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IZ-A6M8        TCGA-P4-A5E7        TCGA-P4-A5EB 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
D43V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1C MUTATED                                  0     0
  CACNA1C WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1C MUTATED                           3    14
  CACNA1C WILD-TYPE                        63   551
D43V12, multiclass
                                  clus
vv                                 CACNA1C MUTATED CACNA1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      3                63
  WHITE                                         14               551
[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"
D43V13, binary
                   cls
clus                  0   1
  CACNA1C MUTATED     1  12
  CACNA1C WILD-TYPE  30 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      1   12
  CACNA1C WILD-TYPE   30  429
                        clus
vv                       CACNA1C MUTATED CACNA1C WILD-TYPE
  HISPANIC OR LATINO                   1                30
  NOT HISPANIC OR LATINO              12               429
[1] 2 2
[1] FALSE

Clustering(44) Variable = PCK1 MUTATION ANALYSIS
D44V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 471 183
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            654 
  PCK1 MUTATED PCK1 WILD-TYPE 
             0            183 
$`PCK1 MUTATED`
TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 TCGA-AL-3472 
       37.38       109.41        51.02        49.97        66.71 

$`PCK1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3331 TCGA-A3-3347 
       24.16        49.02        48.59        36.36        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80        73.08        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       52.87        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        50.24        56.35        47.67 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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 
      107.54        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 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       13.28        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 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
        8.28        12.99        12.46         9.63        70.19        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  PCK1 MUTATED PCK1 WILD-TYPE 
         37.38           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
        109.41         194.79 
  PCK1 MUTATED PCK1 WILD-TYPE 
        51.020         37.235 
[1] "37.4 - 109.4 (51.0)" "0.1 - 194.8 (37.2)" 
[1] "hr="     "3300000"
D44V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         2        1         1        0
  PCK1 WILD-TYPE     323       75       162       88
D44V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              2            323
  STAGE II             1             75
  STAGE III            1            162
  STAGE IV             0             88
[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 335  93 220  10
D44V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            2            335
  T2            2             93
  T3            1            220
  T4            0             10
[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              N0  N1  N2
  PCK1 MUTATED     3   0   0
  PCK1 WILD-TYPE 269  35   6
D44V5, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  N0            3            269
  N1            0             35
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                cls
clus               0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 458  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      5    0
  PCK1 WILD-TYPE  458   78
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            5            458
  1            0             78
[1] 2 2
[1] FALSE
D44V7, binary
                cls
clus               0   1
  PCK1 MUTATED     2   3
  PCK1 WILD-TYPE 227 431
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    3
  PCK1 WILD-TYPE  227  431
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            2            227
  MALE              3            431
[1] 2 2
[1] FALSE
D44V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PCK1 MUTATED                    0                                 4
  PCK1 WILD-TYPE                 66                               432
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PCK1 MUTATED                                       1
  PCK1 WILD-TYPE                                   160
D44V9, multiclass
                                       clus
vv                                      PCK1 MUTATED PCK1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                4            432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[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"
D44V10, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             50 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-4621     TCGA-B8-5158 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5550     TCGA-A4-8310     TCGA-A4-A48D 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-7173 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7838     TCGA-DW-7963     TCGA-G7-6792 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-7773 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-GL-A59T     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
D44V11, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             31 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-7173 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCK1 MUTATED                                  0     0
  PCK1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED                           1     4
  PCK1 WILD-TYPE                        65   561
D44V12, multiclass
                                  clus
vv                                 PCK1 MUTATED PCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             10
  BLACK OR AFRICAN AMERICAN                   1             65
  WHITE                                       4            561
[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"
D44V13, binary
                cls
clus               0   1
  PCK1 MUTATED     0   4
  PCK1 WILD-TYPE  31 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    4
  PCK1 WILD-TYPE   31  437
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            4            437
[1] 2 2
[1] FALSE

Clustering(45) Variable = TPPP MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  TPPP MUTATED     2   1
  TPPP WILD-TYPE 474 182
  TPPP MUTATED TPPP WILD-TYPE 
             3            656 
  TPPP MUTATED TPPP WILD-TYPE 
             1            182 
$`TPPP MUTATED`
TCGA-A3-3385 TCGA-BQ-5883 TCGA-J7-8537 
       65.52        40.83        10.55 

$`TPPP WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3387 TCGA-AK-3425 
       74.76        53.29        43.20        55.76        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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         1.74        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 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-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       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        21.63        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36        12.76        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  TPPP MUTATED TPPP WILD-TYPE 
         10.55           0.07 
  TPPP MUTATED TPPP WILD-TYPE 
         65.52         194.79 
  TPPP MUTATED TPPP WILD-TYPE 
        40.830         37.315 
[1] "10.6 - 65.5 (40.8)" "0.1 - 194.8 (37.3)"
[1] "hr=" "1.3"
D45V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TPPP MUTATED         2        0         1        0
  TPPP WILD-TYPE     323       76       162       88
D45V3, multiclass
           clus
vv          TPPP MUTATED TPPP WILD-TYPE
  STAGE I              2            323
  STAGE II             0             76
  STAGE III            1            162
  STAGE IV             0             88
[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
  TPPP MUTATED     2   0   1   0
  TPPP WILD-TYPE 335  95 220  10
D45V4, multiclass
    clus
vv   TPPP MUTATED TPPP WILD-TYPE
  T1            2            335
  T2            0             95
  T3            1            220
  T4            0             10
[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              N0  N1  N2
  TPPP MUTATED     1   1   0
  TPPP WILD-TYPE 271  34   6
D45V5, multiclass
[1] "Remove cluster labels:" "TPPP MUTATED"          
clus
  TPPP MUTATED TPPP WILD-TYPE 
             2            311 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3313     TCGA-A3-3317     TCGA-A3-3331 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3387     TCGA-AK-3425 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429     TCGA-AK-3430 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3450     TCGA-AK-3451 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5092 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691     TCGA-B0-5692 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620     TCGA-B8-4621 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159     TCGA-B8-5163 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545     TCGA-B8-5546 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5553 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160     TCGA-BP-4162 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331     TCGA-BP-4337 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342     TCGA-BP-4343 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4795 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799     TCGA-BP-4960 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4986 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995     TCGA-BP-5006 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198     TCGA-BP-5199 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638     TCGA-CJ-4639 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891     TCGA-CJ-4892 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904     TCGA-CJ-4918 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033     TCGA-CW-5585 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4856 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
D45V6, binary
                cls
clus               0   1
  TPPP MUTATED     3   0
  TPPP WILD-TYPE 460  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      3    0
  TPPP WILD-TYPE  460   78
   clus
vv  TPPP MUTATED TPPP WILD-TYPE
  0            3            460
  1            0             78
[1] 2 2
[1] FALSE
D45V7, binary
                cls
clus               0   1
  TPPP MUTATED     3   0
  TPPP WILD-TYPE 226 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      3    0
  TPPP WILD-TYPE  226  434
        clus
vv       TPPP MUTATED TPPP WILD-TYPE
  FEMALE            3            226
  MALE              0            434
[1] 2 2
[1] FALSE
D45V8, continuous
[1] "Remove cluster labels:" "TPPP MUTATED"          
clus
  TPPP MUTATED TPPP WILD-TYPE 
             1             92 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8411 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-KO-8413     TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4854 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-Q2-A5QZ 
"TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" "TPPP WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TPPP MUTATED                    0                                 1
  TPPP WILD-TYPE                 66                               435
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TPPP MUTATED                                       2
  TPPP WILD-TYPE                                   159
D45V9, multiclass
                                       clus
vv                                      TPPP MUTATED TPPP WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[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"
D45V10, continuous
D45V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TPPP MUTATED                                  0     1
  TPPP WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TPPP MUTATED                           1     1
  TPPP WILD-TYPE                        65   564
D45V12, multiclass
                                  clus
vv                                 TPPP MUTATED TPPP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                   1             65
  WHITE                                       1            564
[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"
D45V13, binary
                cls
clus               0   1
  TPPP MUTATED     0   2
  TPPP WILD-TYPE  31 439
[1] "tbl2"
                cls
clus             [,1] [,2]
  TPPP MUTATED      0    2
  TPPP WILD-TYPE   31  439
                        clus
vv                       TPPP MUTATED TPPP WILD-TYPE
  HISPANIC OR LATINO                0             31
  NOT HISPANIC OR LATINO            2            439
[1] 2 2
[1] FALSE

Clustering(46) Variable = MLL3 MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    28  10
  MLL3 WILD-TYPE 448 173
  MLL3 MUTATED MLL3 WILD-TYPE 
            38            621 
  MLL3 MUTATED MLL3 WILD-TYPE 
            10            173 
$`MLL3 MUTATED`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KN-8418 
      109.22        98.33       151.96        44.91        47.24       129.37 
TCGA-KN-8424 TCGA-KN-8432 TCGA-KO-8406 TCGA-A3-3370 TCGA-A3-3376 TCGA-B0-4810 
       65.19         2.50       103.40        74.76        55.76        15.72 
TCGA-B0-4945 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B2-5633 TCGA-BP-4164 
       70.52        21.86        52.08        15.95        31.66        32.61 
TCGA-BP-4756 TCGA-BP-4976 TCGA-CJ-5678 TCGA-CJ-5683 TCGA-CZ-4857 TCGA-CZ-5986 
       12.30        53.65        18.87        62.10        47.08        12.26 
TCGA-A4-7997 TCGA-A4-8310 TCGA-B3-4104 TCGA-B9-4114 TCGA-B9-A5W8 TCGA-BQ-5893 
       30.48        25.64        34.49        28.18        17.23         7.92 
TCGA-BQ-7051 TCGA-DW-7840 TCGA-G7-A4TM TCGA-MH-A55W TCGA-P4-A5E7 TCGA-P4-A5EA 
       50.40         3.75         6.38        34.29        87.09         6.61 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       19.73        14.07 

$`MLL3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
       71.41        28.80        54.74        62.37        23.28        28.80 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 
       49.97       123.12        51.06        31.33        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47        10.68       100.47        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      104.55       103.10       130.13        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       90.48        92.55        39.16        24.16        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3385 
       42.97        51.25        74.63        53.29        43.20        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       38.40        82.45        72.89        12.13        40.70         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-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       58.45        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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        36.85        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-B0-5100 
       18.51        15.09        10.95         8.05         2.24        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       38.43        48.82        46.39        56.98        42.41       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
      129.67       133.94        15.78        70.68        85.78        86.47 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
      119.38       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       91.46       126.05        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        24.82        21.57        12.00         5.10         0.85 
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        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        50.14        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        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       48.53         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-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-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        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         6.90        47.11 
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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25        18.15       122.83        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16         0.59        69.21        58.75        14.66       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
        0.23        16.64        29.46        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       70.19        66.71        62.66        67.73         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56        20.25        16.77        20.32        21.07 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       33.83        10.09        30.58        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 
       27.78        30.38        27.65        20.25        99.78        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
       99.12        92.58        17.75 

  MLL3 MUTATED MLL3 WILD-TYPE 
          2.50           0.07 
  MLL3 MUTATED MLL3 WILD-TYPE 
        151.96         194.79 
  MLL3 MUTATED MLL3 WILD-TYPE 
         33.45          37.55 
[1] "2.5 - 152.0 (33.5)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1"  
D46V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MLL3 MUTATED        17        8         9        3
  MLL3 WILD-TYPE     308       68       154       85
D46V3, multiclass
           clus
vv          MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I             17            308
  STAGE II             8             68
  STAGE III            9            154
  STAGE IV             3             85
[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
  MLL3 MUTATED    17  10  11   0
  MLL3 WILD-TYPE 320  85 210  10
D46V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1           17            320
  T2           10             85
  T3           11            210
  T4            0             10
[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              N0  N1  N2
  MLL3 MUTATED    16   3   0
  MLL3 WILD-TYPE 256  32   6
D46V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           16            256
  N1            3             32
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                cls
clus               0   1
  MLL3 MUTATED    21   3
  MLL3 WILD-TYPE 442  75
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     21    3
  MLL3 WILD-TYPE  442   75
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           21            442
  1            3             75
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  MLL3 MUTATED    16  22
  MLL3 WILD-TYPE 213 412
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     16   22
  MLL3 WILD-TYPE  213  412
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           16            213
  MALE             22            412
[1] 2 2
[1] FALSE
D46V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MLL3 MUTATED                    9                                15
  MLL3 WILD-TYPE                 57                               421
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MLL3 MUTATED                                      14
  MLL3 WILD-TYPE                                   147
D46V9, multiclass
                                       clus
vv                                      MLL3 MUTATED MLL3 WILD-TYPE
  KIDNEY CHROMOPHOBE                               9             57
  KIDNEY CLEAR CELL RENAL CARCINOMA               15            421
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           14            147
[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"
D46V10, continuous
D46V11, continuous
[1] "Remove cluster labels:" "MLL3 MUTATED"          
clus
  MLL3 MUTATED MLL3 WILD-TYPE 
             2             30 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117     TCGA-B9-A69E 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-6793     TCGA-G7-6795 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"MLL3 WILD-TYPE" "MLL3 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  0     1
  MLL3 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED                          10    26
  MLL3 WILD-TYPE                        56   539
D46V12, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1              9
  BLACK OR AFRICAN AMERICAN                  10             56
  WHITE                                      26            539
[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"
D46V13, binary
                cls
clus               0   1
  MLL3 MUTATED     1  28
  MLL3 WILD-TYPE  30 413
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      1   28
  MLL3 WILD-TYPE   30  413
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                1             30
  NOT HISPANIC OR LATINO           28            413
[1] 2 2
[1] FALSE

Clustering(47) Variable = PAM MUTATION ANALYSIS
D47V1, survival
               sevent
clus2             0   1
  PAM MUTATED     4   0
  PAM WILD-TYPE 472 183
  PAM MUTATED PAM WILD-TYPE 
            4           655 
  PAM MUTATED PAM WILD-TYPE 
            0           183 
$`PAM MUTATED`
TCGA-B0-5707 TCGA-HE-A5NI TCGA-IA-A40U TCGA-P4-A5E6 
      123.09        11.84        16.80        99.78 

$`PAM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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         6.90        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         1.74        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 
      115.00        46.55        63.25        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-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       107.54        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        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NJ 
        1.05        12.43        17.95        84.89        26.01        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       73.25        25.22        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E7 
       34.29        27.78        30.38        27.65        20.25        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  PAM MUTATED PAM WILD-TYPE 
        11.84          0.07 
  PAM MUTATED PAM WILD-TYPE 
       123.09        194.79 
  PAM MUTATED PAM WILD-TYPE 
        58.29         37.38 
[1] "11.8 - 123.1 (58.3)" "0.1 - 194.8 (37.4)" 
[1] "hr="     "3300000"
D47V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         2        0         2        0
  PAM WILD-TYPE     323       76       161       88
D47V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             2           323
  STAGE II            0            76
  STAGE III           2           161
  STAGE IV            0            88
[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
  PAM MUTATED     3   0   1   0
  PAM WILD-TYPE 334  95 220  10
D47V4, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  T1           3           334
  T2           0            95
  T3           1           220
  T4           0            10
[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             N0  N1  N2
  PAM MUTATED     2   1   0
  PAM WILD-TYPE 270  34   6
D47V5, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  N0           2           270
  N1           1            34
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
               cls
clus              0   1
  PAM MUTATED     2   0
  PAM WILD-TYPE 461  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      2    0
  PAM WILD-TYPE  461   78
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           2           461
  1           0            78
[1] 2 2
[1] FALSE
D47V7, binary
               cls
clus              0   1
  PAM MUTATED     1   3
  PAM WILD-TYPE 228 431
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      1    3
  PAM WILD-TYPE  228  431
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           1           228
  MALE             3           431
[1] 2 2
[1] FALSE
D47V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            92 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KN-8429 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KN-8434    TCGA-KO-8411    TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-4622 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B8-5158    TCGA-CJ-6028    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-4861    TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-5465    TCGA-CZ-5469    TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5906    TCGA-EU-5907    TCGA-A4-7286 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-7828    TCGA-A4-8098    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8517    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5901    TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X    TCGA-IA-A40Y 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PAM MUTATED                    0                                 1
  PAM WILD-TYPE                 66                               435
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PAM MUTATED                                       3
  PAM WILD-TYPE                                   158
D47V9, multiclass
                                       clus
vv                                      PAM MUTATED PAM WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               1           435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           3           158
[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"
D47V10, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            49 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KO-8416    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-4621 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B8-5158    TCGA-B8-5164    TCGA-B8-5550    TCGA-A4-8310    TCGA-A4-A48D 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A44B    TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7963    TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IZ-A6M8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D47V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2    10
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     2
  PAM WILD-TYPE                        65   563
D47V12, multiclass
                                  clus
vv                                 PAM MUTATED PAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            10
  BLACK OR AFRICAN AMERICAN                  1            65
  WHITE                                      2           563
[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"
D47V13, binary
               cls
clus              0   1
  PAM MUTATED     0   3
  PAM WILD-TYPE  31 438
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   31  438
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0            31
  NOT HISPANIC OR LATINO           3           438
[1] 2 2
[1] FALSE

Clustering(48) Variable = GAPDHS MUTATION ANALYSIS
D48V1, survival
                  sevent
clus2                0   1
  GAPDHS MUTATED     3   2
  GAPDHS WILD-TYPE 473 181
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              654 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               2              181 
$`GAPDHS MUTATED`
TCGA-KN-8423 TCGA-B0-5098 TCGA-CJ-4916 TCGA-A4-A48D TCGA-A4-A5Y1 
       25.91        52.08        45.14        12.46        12.99 

$`GAPDHS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        38.56         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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        13.28        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 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
       18.21        19.63        61.05         0.10        21.37        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.13         0.89         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        19.56        21.67        24.56        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77        20.32        21.07        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        74.60        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        20.52        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        84.89 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.76        10.55        18.41        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        99.12        92.58        19.73        17.75        14.07 

  GAPDHS MUTATED GAPDHS WILD-TYPE 
           12.46             0.07 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
           52.08           194.79 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
           25.91            37.43 
[1] "12.5 - 52.1 (25.9)" "0.1 - 194.8 (37.4)"
[1] "hr=" "2.1"
D48V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GAPDHS MUTATED         3        0         2        0
  GAPDHS WILD-TYPE     322       76       161       88
D48V3, multiclass
           clus
vv          GAPDHS MUTATED GAPDHS WILD-TYPE
  STAGE I                3              322
  STAGE II               0               76
  STAGE III              2              161
  STAGE IV               0               88
[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
  GAPDHS MUTATED     4   0   1   0
  GAPDHS WILD-TYPE 333  95 220  10
D48V4, multiclass
    clus
vv   GAPDHS MUTATED GAPDHS WILD-TYPE
  T1              4              333
  T2              0               95
  T3              1              220
  T4              0               10
[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                N0  N1  N2
  GAPDHS MUTATED     1   1   0
  GAPDHS WILD-TYPE 271  34   6
D48V5, multiclass
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               2              311 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8424 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3313       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373       TCGA-A3-3374 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387       TCGA-AK-3425 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429       TCGA-AK-3430 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450       TCGA-AK-3451 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088       TCGA-B0-5092 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691       TCGA-B0-5692 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696       TCGA-B0-5697 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5702 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4621 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159       TCGA-B8-5163 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545       TCGA-B8-5546 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5553 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160       TCGA-BP-4162 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331       TCGA-BP-4337 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342       TCGA-BP-4343 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351       TCGA-BP-4352 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761       TCGA-BP-4768 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787       TCGA-BP-4795 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799       TCGA-BP-4960 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4986 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995       TCGA-BP-5006 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198       TCGA-BP-5199 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638       TCGA-CJ-4639 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891       TCGA-CJ-4892 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904       TCGA-CJ-4918 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033       TCGA-CW-5585 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854       TCGA-CZ-4856 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E       TCGA-AL-3466 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657       TCGA-B9-7268 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879       TCGA-BQ-5880 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887       TCGA-BQ-5888 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5892 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058       TCGA-DW-7963 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793       TCGA-G7-6795 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966       TCGA-GL-A59R 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
D48V6, binary
                  cls
clus                 0   1
  GAPDHS MUTATED     2   0
  GAPDHS WILD-TYPE 461  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      2    0
  GAPDHS WILD-TYPE  461   78
   clus
vv  GAPDHS MUTATED GAPDHS WILD-TYPE
  0              2              461
  1              0               78
[1] 2 2
[1] FALSE
D48V7, binary
                  cls
clus                 0   1
  GAPDHS MUTATED     2   3
  GAPDHS WILD-TYPE 227 431
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      2    3
  GAPDHS WILD-TYPE  227  431
        clus
vv       GAPDHS MUTATED GAPDHS WILD-TYPE
  FEMALE              2              227
  MALE                3              431
[1] 2 2
[1] FALSE
D48V8, continuous
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               1               92 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-EU-5907       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT       TCGA-A4-A57E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GAPDHS MUTATED                    1                                 2
  GAPDHS WILD-TYPE                 65                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GAPDHS MUTATED                                       2
  GAPDHS WILD-TYPE                                   159
D48V9, multiclass
                                       clus
vv                                      GAPDHS MUTATED GAPDHS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[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"
D48V10, continuous
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               1               50 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A57E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
D48V11, continuous
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               1               31 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793       TCGA-G7-6795 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAPDHS MUTATED                                  0     0
  GAPDHS WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAPDHS MUTATED                           2     3
  GAPDHS WILD-TYPE                        64   562
D48V12, multiclass
                                  clus
vv                                 GAPDHS MUTATED GAPDHS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     2               64
  WHITE                                         3              562
[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"
D48V13, binary
                  cls
clus                 0   1
  GAPDHS MUTATED     0   5
  GAPDHS WILD-TYPE  31 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      0    5
  GAPDHS WILD-TYPE   31  436
                        clus
vv                       GAPDHS MUTATED GAPDHS WILD-TYPE
  HISPANIC OR LATINO                  0               31
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(49) Variable = TMCO3 MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  TMCO3 MUTATED     6   1
  TMCO3 WILD-TYPE 470 182
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             652 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              1             182 
$`TMCO3 MUTATED`
TCGA-A3-3331 TCGA-B0-5084 TCGA-BP-4176 TCGA-CJ-4643 TCGA-CZ-4859 TCGA-A4-8515 
       48.82         7.30        64.27        58.95        58.75        23.31 
TCGA-DW-5560 
       48.85 

$`TMCO3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 
       24.16        49.02        48.59        36.36        37.38        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90        34.36        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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-4177 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
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        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        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       122.83        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
      118.85        53.42        75.58        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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-4861 TCGA-CZ-4862 
       46.16         0.59        47.08        69.21        14.66       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        13.28 
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 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       61.05         0.10        21.37        35.18        19.13         0.89 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.97        23.28        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         7.17         3.81        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  TMCO3 MUTATED TMCO3 WILD-TYPE 
           7.30            0.07 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
          64.27          194.79 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
          48.85           37.25 
[1] "7.3 - 64.3 (48.9)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "2.1"
D49V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TMCO3 MUTATED         5        1         0        1
  TMCO3 WILD-TYPE     320       75       163       87
D49V3, multiclass
           clus
vv          TMCO3 MUTATED TMCO3 WILD-TYPE
  STAGE I               5             320
  STAGE II              1              75
  STAGE III             0             163
  STAGE IV              1              87
[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
  TMCO3 MUTATED     5   1   1   0
  TMCO3 WILD-TYPE 332  94 220  10
D49V4, multiclass
    clus
vv   TMCO3 MUTATED TMCO3 WILD-TYPE
  T1             5             332
  T2             1              94
  T3             1             220
  T4             0              10
[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               N0  N1  N2
  TMCO3 MUTATED     3   1   0
  TMCO3 WILD-TYPE 269  34   6
D49V5, multiclass
    clus
vv   TMCO3 MUTATED TMCO3 WILD-TYPE
  N0             3             269
  N1             1              34
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                 cls
clus                0   1
  TMCO3 MUTATED     5   1
  TMCO3 WILD-TYPE 458  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      5    1
  TMCO3 WILD-TYPE  458   77
   clus
vv  TMCO3 MUTATED TMCO3 WILD-TYPE
  0             5             458
  1             1              77
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  TMCO3 MUTATED     4   3
  TMCO3 WILD-TYPE 225 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      4    3
  TMCO3 WILD-TYPE  225  431
        clus
vv       TMCO3 MUTATED TMCO3 WILD-TYPE
  FEMALE             4             225
  MALE               3             431
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "TMCO3 MUTATED"         
clus
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              1              92 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TMCO3 MUTATED                    0                                 5
  TMCO3 WILD-TYPE                 66                               431
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TMCO3 MUTATED                                       2
  TMCO3 WILD-TYPE                                   159
D49V9, multiclass
                                       clus
vv                                      TMCO3 MUTATED TMCO3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[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"
D49V10, continuous
D49V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMCO3 MUTATED                                  1     0
  TMCO3 WILD-TYPE                                1    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMCO3 MUTATED                           0     6
  TMCO3 WILD-TYPE                        66   559
D49V12, multiclass
                                  clus
vv                                 TMCO3 MUTATED TMCO3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              66
  WHITE                                        6             559
[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"
D49V13, binary
                 cls
clus                0   1
  TMCO3 MUTATED     1   4
  TMCO3 WILD-TYPE  30 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      1    4
  TMCO3 WILD-TYPE   30  437
                        clus
vv                       TMCO3 MUTATED TMCO3 WILD-TYPE
  HISPANIC OR LATINO                 1              30
  NOT HISPANIC OR LATINO             4             437
[1] 2 2
[1] FALSE

Clustering(50) Variable = RPL7A MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2               0   1
  RPL7A MUTATED     2   1
  RPL7A WILD-TYPE 474 182
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             656 
  RPL7A MUTATED RPL7A WILD-TYPE 
              1             182 
$`RPL7A MUTATED`
TCGA-BQ-5889 TCGA-DW-7841 TCGA-P4-A5EB 
       10.82        14.63        99.12 

$`RPL7A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78         3.75         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 
       99.78        87.09        42.94         6.61        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  RPL7A MUTATED RPL7A WILD-TYPE 
          10.82            0.07 
  RPL7A MUTATED RPL7A WILD-TYPE 
          99.12          194.79 
  RPL7A MUTATED RPL7A WILD-TYPE 
          14.63           37.43 
[1] "10.8 - 99.1 (14.6)" "0.1 - 194.8 (37.4)"
[1] "hr=" "1.4"
D50V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RPL7A MUTATED         2        0         0        1
  RPL7A WILD-TYPE     323       76       163       87
D50V3, multiclass
           clus
vv          RPL7A MUTATED RPL7A WILD-TYPE
  STAGE I               2             323
  STAGE II              0              76
  STAGE III             0             163
  STAGE IV              1              87
[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
  RPL7A MUTATED     2   0   1   0
  RPL7A WILD-TYPE 335  95 220  10
D50V4, multiclass
    clus
vv   RPL7A MUTATED RPL7A WILD-TYPE
  T1             2             335
  T2             0              95
  T3             1             220
  T4             0              10
[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               N0  N1  N2
  RPL7A MUTATED     0   1   0
  RPL7A WILD-TYPE 272  34   6
D50V5, multiclass
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317      TCGA-A3-3331 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3450 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890      TCGA-BQ-5891 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
D50V6, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   1
  RPL7A WILD-TYPE 463  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    1
  RPL7A WILD-TYPE  463   77
   clus
vv  RPL7A MUTATED RPL7A WILD-TYPE
  0             0             463
  1             1              77
[1] 2 2
[1] FALSE
D50V7, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE 229 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE  229  431
        clus
vv       RPL7A MUTATED RPL7A WILD-TYPE
  FEMALE             0             229
  MALE               3             431
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              92 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RPL7A MUTATED                    0                                 0
  RPL7A WILD-TYPE                 66                               436
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RPL7A MUTATED                                       3
  RPL7A WILD-TYPE                                   158
D50V9, multiclass
                                       clus
vv                                      RPL7A MUTATED RPL7A WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 0             436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[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"
D50V10, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              50 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838      TCGA-DW-7963 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
D50V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL7A MUTATED                                  0     0
  RPL7A WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RPL7A MUTATED                           1     2
  RPL7A WILD-TYPE                        65   563
D50V12, multiclass
                                  clus
vv                                 RPL7A MUTATED RPL7A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              65
  WHITE                                        2             563
[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"
D50V13, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE  31 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE   31  438
                        clus
vv                       RPL7A MUTATED RPL7A WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             3             438
[1] 2 2
[1] FALSE

Clustering(51) Variable = ARHGAP35 MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                  0   1
  ARHGAP35 MUTATED     7   0
  ARHGAP35 WILD-TYPE 469 183
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                652 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 0                183 
$`ARHGAP35 MUTATED`
TCGA-B0-5712 TCGA-B0-5812 TCGA-BP-4756 TCGA-BP-5169 TCGA-CJ-5682 TCGA-CZ-5985 
       89.49       126.05        12.30         6.35       122.83        65.65 
TCGA-A4-7915 
        0.23 

$`ARHGAP35 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
      130.65        79.89       131.15        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        45.37        17.19        25.55        25.91        50.14 
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 
       50.14        16.60         6.38        48.53         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-4758 
       12.23        31.89        11.31        33.99        31.33        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         6.90        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-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.74        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        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       109.84        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 
       51.25       108.56        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       25.25        18.15        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54 
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        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       94.45        10.85        10.22        21.76        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        84.89        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       22.26        21.34        16.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       18.41        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        19.73        17.75        14.07 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.23               0.07 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            126.05             194.79 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            65.650             37.315 
[1] "0.2 - 126.0 (65.7)" "0.1 - 194.8 (37.3)"
[1] "hr="     "9200000"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  ARHGAP35 MUTATED         3        2         0        2
  ARHGAP35 WILD-TYPE     322       74       163       86
D51V3, multiclass
           clus
vv          ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  STAGE I                  3                322
  STAGE II                 2                 74
  STAGE III                0                163
  STAGE IV                 2                 86
[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
  ARHGAP35 MUTATED     3   3   1   0
  ARHGAP35 WILD-TYPE 334  92 220  10
D51V4, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  T1                3                334
  T2                3                 92
  T3                1                220
  T4                0                 10
[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                  N0  N1  N2
  ARHGAP35 MUTATED     5   0   0
  ARHGAP35 WILD-TYPE 267  35   6
D51V5, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  N0                5                267
  N1                0                 35
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     4   2
  ARHGAP35 WILD-TYPE 459  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      4    2
  ARHGAP35 WILD-TYPE  459   76
   clus
vv  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  0                4                459
  1                2                 76
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     3   4
  ARHGAP35 WILD-TYPE 226 430
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      3    4
  ARHGAP35 WILD-TYPE  226  430
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  FEMALE                3                226
  MALE                  4                430
[1] 2 2
[1] FALSE
D51V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ARHGAP35 MUTATED                    0                                 6
  ARHGAP35 WILD-TYPE                 66                               430
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ARHGAP35 MUTATED                                       1
  ARHGAP35 WILD-TYPE                                   160
D51V9, multiclass
                                       clus
vv                                      ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                    6                430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                160
[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"
D51V10, continuous
D51V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP35 MUTATED                                  0     1
  ARHGAP35 WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP35 MUTATED                           2     4
  ARHGAP35 WILD-TYPE                        64   561
D51V12, multiclass
                                  clus
vv                                 ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                  9
  BLACK OR AFRICAN AMERICAN                       2                 64
  WHITE                                           4                561
[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"
D51V13, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     0   5
  ARHGAP35 WILD-TYPE  31 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      0    5
  ARHGAP35 WILD-TYPE   31  436
                        clus
vv                       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  HISPANIC OR LATINO                    0                 31
  NOT HISPANIC OR LATINO                5                436
[1] 2 2
[1] FALSE

Clustering(52) Variable = AHNAK2 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  AHNAK2 MUTATED    23  10
  AHNAK2 WILD-TYPE 453 173
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              626 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              10              173 
$`AHNAK2 MUTATED`
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8337 TCGA-KL-8341 TCGA-KN-8419 TCGA-KN-8423 
       90.48       108.62        44.84        24.79        23.47        25.91 
TCGA-KN-8428 TCGA-KO-8404 TCGA-KO-8413 TCGA-KO-8414 TCGA-AK-3425 TCGA-AK-3454 
       52.27        10.68        99.88       105.60       109.91        28.73 
TCGA-AK-3456 TCGA-B0-4710 TCGA-B0-4847 TCGA-B0-5098 TCGA-B0-5099 TCGA-B4-5843 
       37.58        57.70        26.07        52.08        15.95         0.36 
TCGA-BP-4162 TCGA-BP-4341 TCGA-BP-4981 TCGA-BP-4995 TCGA-BP-5200 TCGA-CJ-4643 
      101.06        52.24        36.07        45.07        34.95        58.95 
TCGA-CJ-4644 TCGA-CW-5583 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5882 TCGA-BQ-7060 
       11.05        81.83        19.56         0.46        21.63         7.04 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-GL-7773 
       74.60        34.19        12.92 

$`AHNAK2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       87.91        25.48        65.19       104.52         3.55         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
       16.67       104.55       103.10       130.13        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       92.55        39.16        24.16        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 
       37.38        48.82        52.93        45.53        88.37        42.97 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       49.28        94.29        83.21        22.45        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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-B0-4848 
       56.68        10.52        10.29        65.29        39.45        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-B0-5100 TCGA-B0-5102 
       10.95         8.05         2.24        21.86        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       112.80       129.67 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      133.94        15.78        70.68        85.78        86.47       119.38 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
      126.05        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       31.66        24.82        21.57        12.00         5.10         0.85 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         5.46         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28        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-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-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         6.90        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       14.93        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-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         1.74        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-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95       115.00        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4868 TCGA-CJ-4869 
       14.17       106.16       114.41        54.61        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        10.72        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00       118.85        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5585 
       62.66       119.64         7.36        64.57        92.02        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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       35.18        19.13         0.89         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47M 
       70.19        66.71        62.66        67.73         2.20        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       17.23         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.17         3.81        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        6.38       194.79         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
            0.36             0.07 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
          109.91           194.79 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
           36.07            37.43 
[1] "0.4 - 109.9 (36.1)" "0.1 - 194.8 (37.4)"
[1] "hr=" "1.1"
D52V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AHNAK2 MUTATED        14        8         6        4
  AHNAK2 WILD-TYPE     311       68       157       84
D52V3, multiclass
           clus
vv          AHNAK2 MUTATED AHNAK2 WILD-TYPE
  STAGE I               14              311
  STAGE II               8               68
  STAGE III              6              157
  STAGE IV               4               84
[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
  AHNAK2 MUTATED    14   9   9   1
  AHNAK2 WILD-TYPE 323  86 212   9
D52V4, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  T1             14              323
  T2              9               86
  T3              9              212
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AHNAK2 MUTATED    18   0   1
  AHNAK2 WILD-TYPE 254  35   5
D52V5, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  N0             18              254
  N1              0               35
  N2              1                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED    24   2
  AHNAK2 WILD-TYPE 439  76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED     24    2
  AHNAK2 WILD-TYPE  439   76
   clus
vv  AHNAK2 MUTATED AHNAK2 WILD-TYPE
  0             24              439
  1              2               76
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED    13  20
  AHNAK2 WILD-TYPE 216 414
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED     13   20
  AHNAK2 WILD-TYPE  216  414
        clus
vv       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  FEMALE             13              216
  MALE               20              414
[1] 2 2
[1] FALSE
D52V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  AHNAK2 MUTATED                   10                                16
  AHNAK2 WILD-TYPE                 56                               420
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AHNAK2 MUTATED                                       7
  AHNAK2 WILD-TYPE                                   154
D52V9, multiclass
                                       clus
vv                                      AHNAK2 MUTATED AHNAK2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                10               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 16              420
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              7              154
[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"
D52V10, continuous
D52V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHNAK2 MUTATED                                  1     2
  AHNAK2 WILD-TYPE                                1     8
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHNAK2 MUTATED                           6    22
  AHNAK2 WILD-TYPE                        60   543
D52V12, multiclass
                                  clus
vv                                 AHNAK2 MUTATED AHNAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         2                8
  BLACK OR AFRICAN AMERICAN                     6               60
  WHITE                                        22              543
[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"
D52V13, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED     2  20
  AHNAK2 WILD-TYPE  29 421
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      2   20
  AHNAK2 WILD-TYPE   29  421
                        clus
vv                       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  HISPANIC OR LATINO                  2               29
  NOT HISPANIC OR LATINO             20              421
[1] 2 2
[1] FALSE

Clustering(53) Variable = JMJD1C MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  JMJD1C MUTATED     9   1
  JMJD1C WILD-TYPE 467 182
  JMJD1C MUTATED JMJD1C WILD-TYPE 
              10              649 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               1              182 
$`JMJD1C MUTATED`
TCGA-KN-8424 TCGA-A3-3357 TCGA-A3-3367 TCGA-BP-4330 TCGA-CJ-4897 TCGA-CW-5581 
       65.19        88.37        74.63        62.07       109.84        92.02 
TCGA-A4-A57E TCGA-BQ-5885 TCGA-G7-6790 TCGA-HE-A5NH 
        8.48        30.28        51.78        26.01 

$`JMJD1C WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67       104.55       103.10       130.13        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
      105.60        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       45.53        42.97        51.25        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       55.76        65.52        20.28       109.91       117.80        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        78.64        49.28        94.29        83.21        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        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73        57.70        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80       129.67       133.94        15.78        70.68        85.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       86.47       119.38       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        91.46       126.05        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       31.96        21.30        31.66        24.82        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        10.72 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98       115.69        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.25 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
      108.56        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15       122.83        62.10        73.35        67.00       118.85 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66       119.64         7.36        64.57 
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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89        10.68         4.01        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       17.95        84.89        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 
TCGA-Q2-A5QZ 
       14.07 

  JMJD1C MUTATED JMJD1C WILD-TYPE 
            8.48             0.07 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
          109.84           194.79 
  JMJD1C MUTATED JMJD1C WILD-TYPE 
           63.63            37.25 
[1] "8.5 - 109.8 (63.6)" "0.1 - 194.8 (37.2)"
[1] "hr=" "3.8"
D53V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  JMJD1C MUTATED         5        1         3        1
  JMJD1C WILD-TYPE     320       75       160       87
D53V3, multiclass
           clus
vv          JMJD1C MUTATED JMJD1C WILD-TYPE
  STAGE I                5              320
  STAGE II               1               75
  STAGE III              3              160
  STAGE IV               1               87
[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
  JMJD1C MUTATED     5   2   3   0
  JMJD1C WILD-TYPE 332  93 218  10
D53V4, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  T1              5              332
  T2              2               93
  T3              3              218
  T4              0               10
[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                N0  N1  N2
  JMJD1C MUTATED     6   0   0
  JMJD1C WILD-TYPE 266  35   6
D53V5, multiclass
    clus
vv   JMJD1C MUTATED JMJD1C WILD-TYPE
  N0              6              266
  N1              0               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                  cls
clus                 0   1
  JMJD1C MUTATED     6   1
  JMJD1C WILD-TYPE 457  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED      6    1
  JMJD1C WILD-TYPE  457   77
   clus
vv  JMJD1C MUTATED JMJD1C WILD-TYPE
  0              6              457
  1              1               77
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  JMJD1C MUTATED     3   7
  JMJD1C WILD-TYPE 226 427
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED      3    7
  JMJD1C WILD-TYPE  226  427
        clus
vv       JMJD1C MUTATED JMJD1C WILD-TYPE
  FEMALE              3              226
  MALE                7              427
[1] 2 2
[1] FALSE
D53V8, continuous
[1] "Remove cluster labels:" "JMJD1C MUTATED"        
clus
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               2               91 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8411 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4854 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-4862 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-EU-5907       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6789       TCGA-G7-6792       TCGA-G7-6793 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  JMJD1C MUTATED                    1                                 5
  JMJD1C WILD-TYPE                 65                               431
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  JMJD1C MUTATED                                       4
  JMJD1C WILD-TYPE                                   157
D53V9, multiclass
                                       clus
vv                                      JMJD1C MUTATED JMJD1C WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  5              431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              157
[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"
D53V10, continuous
[1] "Remove cluster labels:" "JMJD1C MUTATED"        
clus
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               1               50 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-4621       TCGA-B8-5158 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5550       TCGA-A4-8310       TCGA-A4-A48D 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7838       TCGA-DW-7963       TCGA-G7-6792 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-7773 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-GL-A59T       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
D53V11, continuous
[1] "Remove cluster labels:" "JMJD1C MUTATED"        
clus
  JMJD1C MUTATED JMJD1C WILD-TYPE 
               1               31 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-6793       TCGA-G7-6795 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-G7-7501       TCGA-GL-7773       TCGA-HE-A5NI       TCGA-IA-A40U 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" "JMJD1C WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  JMJD1C MUTATED                                  0     0
  JMJD1C WILD-TYPE                                2    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  JMJD1C MUTATED                           1     8
  JMJD1C WILD-TYPE                        65   557
D53V12, multiclass
                                  clus
vv                                 JMJD1C MUTATED JMJD1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               10
  BLACK OR AFRICAN AMERICAN                     1               65
  WHITE                                         8              557
[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"
D53V13, binary
                  cls
clus                 0   1
  JMJD1C MUTATED     2   6
  JMJD1C WILD-TYPE  29 435
[1] "tbl2"
                  cls
clus               [,1] [,2]
  JMJD1C MUTATED      2    6
  JMJD1C WILD-TYPE   29  435
                        clus
vv                       JMJD1C MUTATED JMJD1C WILD-TYPE
  HISPANIC OR LATINO                  2               29
  NOT HISPANIC OR LATINO              6              435
[1] 2 2
[1] FALSE

Clustering(54) Variable = TTLL6 MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  TTLL6 MUTATED     5   1
  TTLL6 WILD-TYPE 471 182
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              6             653 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              1             182 
$`TTLL6 MUTATED`
TCGA-KL-8325 TCGA-KO-8409 TCGA-B4-5844 TCGA-DV-5569 TCGA-B9-4114 TCGA-DZ-6131 
       23.84       104.55         0.23        11.67        28.18        79.86 

$`TTLL6 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67       103.10       130.13        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       96.62        90.48        92.55        39.16        24.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       88.37        42.97        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       43.20        55.76        65.52        20.28       109.91       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       94.19        46.78        78.64        49.28        94.29        83.21 
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        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73        57.70 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        58.45        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        10.52        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 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       42.41       112.80       129.67       133.94        15.78        70.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       85.78        86.47       119.38       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
      131.15        89.49        91.46       126.05        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        31.96        21.30        31.66        24.82        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         0.85         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        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       45.37        17.19        25.55        25.91        50.14        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        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-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         6.90        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         1.74        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       115.00        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       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       10.72        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00       118.85        53.42        75.58        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-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-5574 TCGA-DV-5575 
       62.63        13.28        45.96        12.16        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 
       19.63        61.05         0.10        21.37        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
        0.89         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       62.66        67.73         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
       20.25        16.77        20.32        21.07        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       30.58        34.49        12.46        50.50        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       74.60        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       20.52        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        84.89        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        22.26        21.34        16.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        18.41        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       99.12        92.58        19.73        17.75        14.07 

  TTLL6 MUTATED TTLL6 WILD-TYPE 
           0.23            0.07 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
         104.55          194.79 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
          26.01           37.48 
[1] "0.2 - 104.5 (26.0)" "0.1 - 194.8 (37.5)"
[1] "hr=" "1.5"
D54V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TTLL6 MUTATED         1        3         1        0
  TTLL6 WILD-TYPE     324       73       162       88
D54V3, multiclass
           clus
vv          TTLL6 MUTATED TTLL6 WILD-TYPE
  STAGE I               1             324
  STAGE II              3              73
  STAGE III             1             162
  STAGE IV              0              88
[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
  TTLL6 MUTATED     1   4   1   0
  TTLL6 WILD-TYPE 336  91 220  10
D54V4, multiclass
    clus
vv   TTLL6 MUTATED TTLL6 WILD-TYPE
  T1             1             336
  T2             4              91
  T3             1             220
  T4             0              10
[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               N0  N1  N2
  TTLL6 MUTATED     3   0   0
  TTLL6 WILD-TYPE 269  35   6
D54V5, multiclass
    clus
vv   TTLL6 MUTATED TTLL6 WILD-TYPE
  N0             3             269
  N1             0              35
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                 cls
clus                0   1
  TTLL6 MUTATED     4   0
  TTLL6 WILD-TYPE 459  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      4    0
  TTLL6 WILD-TYPE  459   78
   clus
vv  TTLL6 MUTATED TTLL6 WILD-TYPE
  0             4             459
  1             0              78
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  TTLL6 MUTATED     3   3
  TTLL6 WILD-TYPE 226 431
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      3    3
  TTLL6 WILD-TYPE  226  431
        clus
vv       TTLL6 MUTATED TTLL6 WILD-TYPE
  FEMALE             3             226
  MALE               3             431
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              2              91 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B8-4143      TCGA-B8-4622 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854      TCGA-CZ-4856 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907      TCGA-A4-7286 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TTLL6 MUTATED                    2                                 2
  TTLL6 WILD-TYPE                 64                               434
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TTLL6 MUTATED                                       2
  TTLL6 WILD-TYPE                                   159
D54V9, multiclass
                                       clus
vv                                      TTLL6 MUTATED TTLL6 WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                 2             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[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"
D54V10, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              2              49 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8416      TCGA-AK-3445      TCGA-AK-3451 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-4146      TCGA-B8-4621      TCGA-B8-5158      TCGA-B8-5164 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-5550      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7963      TCGA-G7-6792      TCGA-G7-6793 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"TTLL6 WILD-TYPE" 
D54V11, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              2              30 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-AK-3445 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550      TCGA-A4-A48D 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4117      TCGA-B9-A69E      TCGA-DW-5561 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTLL6 MUTATED                                  0     0
  TTLL6 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTLL6 MUTATED                           1     5
  TTLL6 WILD-TYPE                        65   560
D54V12, multiclass
                                  clus
vv                                 TTLL6 MUTATED TTLL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    1              65
  WHITE                                        5             560
[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"
D54V13, binary
                 cls
clus                0   1
  TTLL6 MUTATED     0   4
  TTLL6 WILD-TYPE  31 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      0    4
  TTLL6 WILD-TYPE   31  437
                        clus
vv                       TTLL6 MUTATED TTLL6 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             4             437
[1] 2 2
[1] FALSE

Clustering(55) Variable = AMAC1L3 MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  AMAC1L3 MUTATED     8   0
  AMAC1L3 WILD-TYPE 468 183
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                8               651 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                0               183 
$`AMAC1L3 MUTATED`
TCGA-KL-8335 TCGA-KL-8337 TCGA-KM-8477 TCGA-KN-8431 TCGA-KN-8436 TCGA-B0-5693 
       92.55        44.84        51.06        19.33        42.35       133.94 
TCGA-BQ-5890 TCGA-GL-A4EM 
        7.66         1.05 

$`AMAC1L3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8639 
       44.91        28.80        47.24        49.97       123.12        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 
      104.52         3.55         0.99        52.27        87.12         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      130.13        99.88       105.60        96.62        90.48        92.55 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        24.16        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-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91       117.80        73.08       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       49.28        94.29        83.21        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       38.40        82.45        72.89        12.13        40.70         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-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73        57.70        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       58.45        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       112.80       129.67 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 
        0.10        21.37        35.18        19.13         0.89         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        70.19        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56        20.25        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.32        21.07        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23        17.23         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25        10.82         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        48.85        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        84.89        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25        25.22        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD 
       21.34        16.34        12.36        12.76        10.55        18.41 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       19.73        17.75        14.07 

  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
             1.05              0.07 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
           133.94            194.79 
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
           43.595            37.250 
[1] "1.1 - 133.9 (43.6)" "0.1 - 194.8 (37.2)"
[1] "hr="     "9100000"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  AMAC1L3 MUTATED         3        3         2        0
  AMAC1L3 WILD-TYPE     322       73       161       88
D55V3, multiclass
           clus
vv          AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  STAGE I                 3               322
  STAGE II                3                73
  STAGE III               2               161
  STAGE IV                0                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  AMAC1L3 MUTATED     3   3   2   0
  AMAC1L3 WILD-TYPE 334  92 219  10
D55V4, multiclass
    clus
vv   AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  T1               3               334
  T2               3                92
  T3               2               219
  T4               0                10
[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                 N0  N1  N2
  AMAC1L3 MUTATED     3   0   0
  AMAC1L3 WILD-TYPE 269  35   6
D55V5, multiclass
    clus
vv   AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  N0               3               269
  N1               0                35
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  AMAC1L3 MUTATED     4   0
  AMAC1L3 WILD-TYPE 459  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      4    0
  AMAC1L3 WILD-TYPE  459   78
   clus
vv  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  0               4               459
  1               0                78
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  AMAC1L3 MUTATED     2   6
  AMAC1L3 WILD-TYPE 227 428
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      2    6
  AMAC1L3 WILD-TYPE  227  428
        clus
vv       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  FEMALE               2               227
  MALE                 6               428
[1] 2 2
[1] FALSE
D55V8, continuous
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                92 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8639 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8411        TCGA-KO-8413 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4854        TCGA-CZ-4856 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566        TCGA-DV-5568 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575        TCGA-DV-5576 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-IA-A40U 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  AMAC1L3 MUTATED                    5                                 1
  AMAC1L3 WILD-TYPE                 61                               435
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AMAC1L3 MUTATED                                       2
  AMAC1L3 WILD-TYPE                                   159
D55V9, multiclass
                                       clus
vv                                      AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  5                61
  KIDNEY CLEAR CELL RENAL CARCINOMA                   1               435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               159
[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"
D55V10, continuous
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                50 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8341        TCGA-KL-8345 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445        TCGA-AK-3451 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158        TCGA-B8-5164 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B8-5550        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7838        TCGA-DW-7963        TCGA-G7-6792 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7773 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IZ-A6M8        TCGA-P4-A5E7        TCGA-P4-A5EB 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
D55V11, continuous
[1] "Remove cluster labels:" "AMAC1L3 MUTATED"       
clus
  AMAC1L3 MUTATED AMAC1L3 WILD-TYPE 
                1                31 
       TCGA-KL-8330        TCGA-KL-8341        TCGA-KL-8345        TCGA-KM-8639 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409        TCGA-AK-3445 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-AK-3451        TCGA-B8-5158        TCGA-B8-5550        TCGA-A4-A48D 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7963        TCGA-G7-6793        TCGA-G7-6795 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-G7-7501        TCGA-GL-7773        TCGA-HE-A5NI        TCGA-IA-A40U 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" "AMAC1L3 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMAC1L3 MUTATED                                  0     0
  AMAC1L3 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AMAC1L3 MUTATED                           1     6
  AMAC1L3 WILD-TYPE                        65   559
D55V12, multiclass
                                  clus
vv                                 AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                65
  WHITE                                          6               559
[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"
D55V13, binary
                   cls
clus                  0   1
  AMAC1L3 MUTATED     0   5
  AMAC1L3 WILD-TYPE  31 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMAC1L3 MUTATED      0    5
  AMAC1L3 WILD-TYPE   31  436
                        clus
vv                       AMAC1L3 MUTATED AMAC1L3 WILD-TYPE
  HISPANIC OR LATINO                   0                31
  NOT HISPANIC OR LATINO               5               436
[1] 2 2
[1] FALSE

Clustering(56) Variable = TRAPPC9 MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  TRAPPC9 MUTATED     5   0
  TRAPPC9 WILD-TYPE 471 183
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                5               654 
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                0               183 
$`TRAPPC9 MUTATED`
TCGA-KO-8414 TCGA-BP-4782 TCGA-A4-7996 TCGA-HE-A5NH TCGA-Q2-A5QZ 
      105.60        11.64        16.64        26.01        14.07 

$`TRAPPC9 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
       99.88        96.62        90.48        92.55        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       45.53        88.37        42.97        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       53.29        43.20        55.76        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80        73.08       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
      109.51        94.19        46.78        78.64        49.28        94.29 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       83.21        28.73        22.45        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        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 
       57.70        43.96         6.64         3.25        58.45        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        10.52        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        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       56.98        42.41       112.80       129.67       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       70.68        85.78        86.47       119.38       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       79.89       131.15        89.49        91.46       126.05        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        31.96        21.30        31.66        24.82 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         0.85         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 
       42.71        25.05        45.37        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       50.14        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        50.14        16.60         6.38        48.53         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-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         6.90        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         1.74        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       115.00 
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       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        10.72        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98       115.69        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       109.84        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        51.25       108.56        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00       118.85        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-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       107.54        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        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
        4.18        18.21        19.63        61.05         0.10        21.37 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7997 
       35.18        19.13         0.89         7.82         0.23        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       66.71        62.66        67.73         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56        20.25        16.77        20.32        21.07        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23        17.23         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        48.85        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       17.95        84.89        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       12.36        12.76        10.55        18.41        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        99.12        92.58        19.73        17.75 

  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
            11.64              0.07 
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
           105.60            194.79 
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
           16.640            37.515 
[1] "11.6 - 105.6 (16.6)" "0.1 - 194.8 (37.5)" 
[1] "hr="     "3300000"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  TRAPPC9 MUTATED         3        1         1        0
  TRAPPC9 WILD-TYPE     322       75       162       88
D56V3, multiclass
           clus
vv          TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  STAGE I                 3               322
  STAGE II                1                75
  STAGE III               1               162
  STAGE IV                0                88
[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
  TRAPPC9 MUTATED     3   1   1   0
  TRAPPC9 WILD-TYPE 334  94 220  10
D56V4, multiclass
    clus
vv   TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  T1               3               334
  T2               1                94
  T3               1               220
  T4               0                10
[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                 N0  N1  N2
  TRAPPC9 MUTATED     1   0   0
  TRAPPC9 WILD-TYPE 271  35   6
D56V5, multiclass
[1] "Remove cluster labels:" "TRAPPC9 MUTATED"       
clus
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                1               312 
       TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328        TCGA-KL-8329 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332        TCGA-KL-8333 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336        TCGA-KL-8337 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340        TCGA-KL-8341 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8430        TCGA-KO-8405        TCGA-KO-8406 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8410 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KO-8413        TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A3-3313        TCGA-A3-3317        TCGA-A3-3331        TCGA-A3-3347 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3362 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A3-3367        TCGA-A3-3370        TCGA-A3-3373        TCGA-A3-3374 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A3-3376        TCGA-A3-3385        TCGA-A3-3387        TCGA-AK-3425 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AK-3427        TCGA-AK-3428        TCGA-AK-3429        TCGA-AK-3430 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AK-3436        TCGA-AK-3443        TCGA-AK-3450        TCGA-AK-3451 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AK-3456        TCGA-B0-4690        TCGA-B0-4691        TCGA-B0-4693 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4710        TCGA-B0-4810        TCGA-B0-4811 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-4814        TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4823 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4833        TCGA-B0-4837 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B0-4839        TCGA-B0-4842        TCGA-B0-4843 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-4846        TCGA-B0-4852        TCGA-B0-4945        TCGA-B0-5075 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5077        TCGA-B0-5080        TCGA-B0-5081        TCGA-B0-5083 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088        TCGA-B0-5092 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5094        TCGA-B0-5095        TCGA-B0-5096        TCGA-B0-5097 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107        TCGA-B0-5108 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5109        TCGA-B0-5110        TCGA-B0-5113        TCGA-B0-5115 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5116        TCGA-B0-5119        TCGA-B0-5120        TCGA-B0-5121 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5691        TCGA-B0-5692 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696        TCGA-B0-5697 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5707 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B0-5710        TCGA-B0-5712        TCGA-B0-5713        TCGA-B2-5633 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4148        TCGA-B8-4151 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620        TCGA-B8-4621 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159        TCGA-B8-5163 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545        TCGA-B8-5546 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551        TCGA-B8-5553 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4158        TCGA-BP-4159        TCGA-BP-4160        TCGA-BP-4162 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4163        TCGA-BP-4165        TCGA-BP-4166        TCGA-BP-4169 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4170        TCGA-BP-4173        TCGA-BP-4174        TCGA-BP-4326 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4329        TCGA-BP-4330        TCGA-BP-4331        TCGA-BP-4337 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4338        TCGA-BP-4340        TCGA-BP-4342        TCGA-BP-4343 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4345        TCGA-BP-4346        TCGA-BP-4351        TCGA-BP-4352 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4354        TCGA-BP-4756        TCGA-BP-4761        TCGA-BP-4768 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4770        TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4795 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4797        TCGA-BP-4798        TCGA-BP-4799        TCGA-BP-4960 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4964        TCGA-BP-4967        TCGA-BP-4968        TCGA-BP-4970 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4971        TCGA-BP-4974        TCGA-BP-4985        TCGA-BP-4986 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4995        TCGA-BP-5006 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-5007        TCGA-BP-5010        TCGA-BP-5169        TCGA-BP-5182 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-5186        TCGA-BP-5191        TCGA-BP-5198        TCGA-BP-5199 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BP-5201        TCGA-CJ-4636        TCGA-CJ-4638        TCGA-CJ-4639 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CJ-4640        TCGA-CJ-4643        TCGA-CJ-4644        TCGA-CJ-4868 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CJ-4869        TCGA-CJ-4872        TCGA-CJ-4873        TCGA-CJ-4874 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CJ-4876        TCGA-CJ-4890        TCGA-CJ-4891        TCGA-CJ-4892 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CJ-4894        TCGA-CJ-4900        TCGA-CJ-4904        TCGA-CJ-4918 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CJ-5678        TCGA-CJ-6030        TCGA-CJ-6033        TCGA-CW-5585 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CW-5591        TCGA-CW-6087        TCGA-CZ-4854        TCGA-CZ-4856 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-5451 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5454        TCGA-CZ-5456        TCGA-CZ-5467 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5984        TCGA-CZ-5985 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-5986        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-A4-7583 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E        TCGA-A4-A5Y1 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656        TCGA-B1-A657 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7058 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846        TCGA-GL-7966 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y        TCGA-J7-6720 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-J7-8537        TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
D56V6, binary
                   cls
clus                  0   1
  TRAPPC9 MUTATED     2   0
  TRAPPC9 WILD-TYPE 461  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAPPC9 MUTATED      2    0
  TRAPPC9 WILD-TYPE  461   78
   clus
vv  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  0               2               461
  1               0                78
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  TRAPPC9 MUTATED     4   1
  TRAPPC9 WILD-TYPE 225 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAPPC9 MUTATED      4    1
  TRAPPC9 WILD-TYPE  225  433
        clus
vv       TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  FEMALE               4               225
  MALE                 1               433
[1] 2 2
[1] FALSE
D56V8, continuous
[1] "Remove cluster labels:" "TRAPPC9 MUTATED"       
clus
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                1                92 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8411 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KO-8413        TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4854 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-4862 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-EU-5907        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TRAPPC9 MUTATED                    1                                 1
  TRAPPC9 WILD-TYPE                 65                               435
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TRAPPC9 MUTATED                                       3
  TRAPPC9 WILD-TYPE                                   158
D56V9, multiclass
                                       clus
vv                                      TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   1               435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               158
[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"
D56V10, continuous
[1] "Remove cluster labels:" "TRAPPC9 MUTATED"       
clus
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                1                50 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AK-3451        TCGA-B8-4146        TCGA-B8-4621        TCGA-B8-5158 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-5550        TCGA-A4-8310        TCGA-A4-A48D 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A69E 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-DW-7963 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A59T        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-HE-A5NK        TCGA-IA-A40U        TCGA-IZ-A6M8        TCGA-P4-A5E7 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
D56V11, continuous
[1] "Remove cluster labels:" "TRAPPC9 MUTATED"       
clus
  TRAPPC9 MUTATED TRAPPC9 WILD-TYPE 
                1                31 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3451        TCGA-B8-5158        TCGA-B8-5550 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-G7-6793 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-7773        TCGA-HE-A5NI 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-P4-A5E6        TCGA-PJ-A5Z9 
"TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" "TRAPPC9 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TRAPPC9 MUTATED                                  0     0
  TRAPPC9 WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  TRAPPC9 MUTATED                           1     3
  TRAPPC9 WILD-TYPE                        65   562
D56V12, multiclass
                                  clus
vv                                 TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                10
  BLACK OR AFRICAN AMERICAN                      1                65
  WHITE                                          3               562
[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"
D56V13, binary
                   cls
clus                  0   1
  TRAPPC9 MUTATED     0   3
  TRAPPC9 WILD-TYPE  31 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TRAPPC9 MUTATED      0    3
  TRAPPC9 WILD-TYPE   31  438
                        clus
vv                       TRAPPC9 MUTATED TRAPPC9 WILD-TYPE
  HISPANIC OR LATINO                   0                31
  NOT HISPANIC OR LATINO               3               438
[1] 2 2
[1] FALSE

Clustering(57) Variable = MED16 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  MED16 MUTATED     2   1
  MED16 WILD-TYPE 474 182
  MED16 MUTATED MED16 WILD-TYPE 
              3             656 
  MED16 MUTATED MED16 WILD-TYPE 
              1             182 
$`MED16 MUTATED`
TCGA-CZ-5986 TCGA-BQ-5890 TCGA-G7-6789 
       12.26         7.66         4.01 

$`MED16 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
      103.40        92.71        16.67       104.55       103.10       130.13 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       99.88       105.60        96.62        90.48        92.55        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       24.16        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-A3-3367 
       52.93        45.53        88.37        42.97        51.25        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 
       74.76        53.29        43.20        55.76        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91       117.80        73.08       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61       109.51        94.19        46.78        78.64        49.28 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       94.29        83.21        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73        57.70        43.96         6.64         3.25        58.45 
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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 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        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       46.39        56.98        42.41       112.80       129.67       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        70.68        85.78        86.47       119.38       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      130.65        79.89       131.15        89.49        91.46       126.05 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       24.82        21.57        12.00         5.10         0.85         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        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        50.14        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        50.14        16.60         6.38        48.53 
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-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-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-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         6.90 
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         1.74 
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       115.00        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 
      106.16       114.41        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        10.72        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-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       109.84 
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        51.25       108.56 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
      122.83        62.10        73.35        67.00       118.85        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66       119.64         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       107.54        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        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        13.28        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 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7584 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 
       21.37        35.18        19.13         0.89         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        70.19        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56        20.25        16.77        20.32 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       21.07        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23        17.23         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25        10.82         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        48.85        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        24.89        10.68        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        84.89        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       25.22        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       16.34        12.36        12.76        10.55        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.09        42.94         6.61        99.12        92.58        19.73 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  MED16 MUTATED MED16 WILD-TYPE 
           4.01            0.07 
  MED16 MUTATED MED16 WILD-TYPE 
          12.26          194.79 
  MED16 MUTATED MED16 WILD-TYPE 
          7.660          37.515 
[1] "4.0 - 12.3 (7.7)"   "0.1 - 194.8 (37.5)"
[1] "hr=" "6.4"
D57V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MED16 MUTATED         1        0         2        1
  MED16 WILD-TYPE     324       76       161       87
D57V3, multiclass
           clus
vv          MED16 MUTATED MED16 WILD-TYPE
  STAGE I               1             324
  STAGE II              0              76
  STAGE III             2             161
  STAGE IV              1              87
[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
  MED16 MUTATED     1   0   3   0
  MED16 WILD-TYPE 336  95 218  10
D57V4, multiclass
    clus
vv   MED16 MUTATED MED16 WILD-TYPE
  T1             1             336
  T2             0              95
  T3             3             218
  T4             0              10
[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               N0  N1  N2
  MED16 MUTATED     2   0   1
  MED16 WILD-TYPE 270  35   5
D57V5, multiclass
    clus
vv   MED16 MUTATED MED16 WILD-TYPE
  N0             2             270
  N1             0              35
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                 cls
clus                0   1
  MED16 MUTATED     3   0
  MED16 WILD-TYPE 460  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      3    0
  MED16 WILD-TYPE  460   78
   clus
vv  MED16 MUTATED MED16 WILD-TYPE
  0             3             460
  1             0              78
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus                0   1
  MED16 MUTATED     2   2
  MED16 WILD-TYPE 227 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      2    2
  MED16 WILD-TYPE  227  432
        clus
vv       MED16 MUTATED MED16 WILD-TYPE
  FEMALE             2             227
  MALE               2             432
[1] 2 2
[1] FALSE
D57V8, continuous
[1] "Remove cluster labels:" "MED16 MUTATED"         
clus
  MED16 MUTATED MED16 WILD-TYPE 
              1              92 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8411 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4854 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6792 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-IA-A40U 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" "MED16 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MED16 MUTATED                    0                                 1
  MED16 WILD-TYPE                 66                               435
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MED16 MUTATED                                       3
  MED16 WILD-TYPE                                   158
D57V9, multiclass
                                       clus
vv                                      MED16 MUTATED MED16 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 1             435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[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"
D57V10, continuous
D57V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED16 MUTATED                                  0     0
  MED16 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED16 MUTATED                           0     3
  MED16 WILD-TYPE                        66   562
D57V12, multiclass
                                  clus
vv                                 MED16 MUTATED MED16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              10
  BLACK OR AFRICAN AMERICAN                    0              66
  WHITE                                        3             562
[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"
D57V13, binary
                 cls
clus                0   1
  MED16 MUTATED     0   2
  MED16 WILD-TYPE  31 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      0    2
  MED16 WILD-TYPE   31  439
                        clus
vv                       MED16 MUTATED MED16 WILD-TYPE
  HISPANIC OR LATINO                 0              31
  NOT HISPANIC OR LATINO             2             439
[1] 2 2
[1] FALSE
