[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/22506733/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/22815577/transformed.cor.cli.txt"

nPatients in clinical file=941, in cluster file=824, common to both=784
[1] "Reduce the number of clustering variables from 71 to 70."
[1]  70 784
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            38            746 
  TP53 MUTATED TP53 WILD-TYPE 
            38            746 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            28            756 
  PTEN MUTATED PTEN WILD-TYPE 
            28            756 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             61             723 
  SETD2 MUTATED SETD2 WILD-TYPE 
             61             723 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            143             641 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            143             641 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            12            772 
  NEFH MUTATED NEFH WILD-TYPE 
            12            772 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          196           588 
  VHL MUTATED VHL WILD-TYPE 
          196           588 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           16           768 
  NF2 MUTATED NF2 WILD-TYPE 
           16           768 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           25           759 
  MET MUTATED MET WILD-TYPE 
           25           759 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             757 
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             757 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            34            750 
  MTOR MUTATED MTOR WILD-TYPE 
            34            750 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              14              770 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              14              770 
[1] "AR MUTATION ANALYSIS"
[1] 3
  AR MUTATED AR WILD-TYPE 
          15          769 
  AR MUTATED AR WILD-TYPE 
          15          769 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             15             769 
  STAG2 MUTATED STAG2 WILD-TYPE 
             15             769 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
             6            778 
  KRAS MUTATED KRAS WILD-TYPE 
             6            778 
[1] "SLC6A14 MUTATION ANALYSIS"
[1] 3
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                4               780 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                4               780 
[1] "SMARCA4 MUTATION ANALYSIS"
[1] 3
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               20               764 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               20               764 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              772 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              772 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              18              766 
  ARID1A MUTATED ARID1A WILD-TYPE 
              18              766 
[1] "BCLAF1 MUTATION ANALYSIS"
[1] 3
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              10              774 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              10              774 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           20           764 
  ATM MUTATED ATM WILD-TYPE 
           20           764 
[1] "CACNA1C MUTATION ANALYSIS"
[1] 3
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               15               769 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               15               769 
[1] "PARD6B MUTATION ANALYSIS"
[1] 3
  PARD6B MUTATED PARD6B WILD-TYPE 
               8              776 
  PARD6B MUTATED PARD6B WILD-TYPE 
               8              776 
[1] "CUL3 MUTATION ANALYSIS"
[1] 3
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            768 
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            768 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15              769 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15              769 
[1] "SMARCB1 MUTATION ANALYSIS"
[1] 3
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                9               775 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                9               775 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
             13             771 
  PCF11 MUTATED PCF11 WILD-TYPE 
             13             771 
[1] "WASL MUTATION ANALYSIS"
[1] 3
  WASL MUTATED WASL WILD-TYPE 
             8            776 
  WASL MUTATED WASL WILD-TYPE 
             8            776 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              11              773 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              11              773 
[1] "KIAA0922 MUTATION ANALYSIS"
[1] 3
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 7                777 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 7                777 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             779 
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             779 
[1] "ACSF2 MUTATION ANALYSIS"
[1] 3
  ACSF2 MUTATED ACSF2 WILD-TYPE 
             11             773 
  ACSF2 MUTATED ACSF2 WILD-TYPE 
             11             773 
[1] "WDR52 MUTATION ANALYSIS"
[1] 3
  WDR52 MUTATED WDR52 WILD-TYPE 
              9             775 
  WDR52 MUTATED WDR52 WILD-TYPE 
              9             775 
[1] "ALMS1 MUTATION ANALYSIS"
[1] 3
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             14             770 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             14             770 
[1] "TXNIP MUTATION ANALYSIS"
[1] 3
  TXNIP MUTATED TXNIP WILD-TYPE 
              8             776 
  TXNIP MUTATED TXNIP WILD-TYPE 
              8             776 
[1] "NUDT11 MUTATION ANALYSIS"
[1] 3
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              779 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              779 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             9            775 
  PCK1 MUTATED PCK1 WILD-TYPE 
             9            775 
[1] "RAI1 MUTATION ANALYSIS"
[1] 3
  RAI1 MUTATED RAI1 WILD-TYPE 
            11            773 
  RAI1 MUTATED RAI1 WILD-TYPE 
            11            773 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            4           780 
  PAM MUTATED PAM WILD-TYPE 
            4           780 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             771 
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             771 
[1] "GLS MUTATION ANALYSIS"
[1] 3
  GLS MUTATED GLS WILD-TYPE 
            9           775 
  GLS MUTATED GLS WILD-TYPE 
            9           775 
[1] "EPS15L1 MUTATION ANALYSIS"
[1] 3
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
               10               774 
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
               10               774 
[1] "NOM1 MUTATION ANALYSIS"
[1] 3
  NOM1 MUTATED NOM1 WILD-TYPE 
             6            778 
  NOM1 MUTATED NOM1 WILD-TYPE 
             6            778 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             776 
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             776 
[1] "ARHGAP35 MUTATION ANALYSIS"
[1] 3
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                777 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                777 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              779 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              779 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            20            764 
  FAT1 MUTATED FAT1 WILD-TYPE 
            20            764 
[1] "FAM178A MUTATION ANALYSIS"
[1] 3
  FAM178A MUTATED FAM178A WILD-TYPE 
                8               776 
  FAM178A MUTATED FAM178A WILD-TYPE 
                8               776 
[1] "TCEB1 MUTATION ANALYSIS"
[1] 3
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              4             780 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              4             780 
[1] "PODXL MUTATION ANALYSIS"
[1] 3
  PODXL MUTATED PODXL WILD-TYPE 
              6             778 
  PODXL MUTATED PODXL WILD-TYPE 
              6             778 
[1] "DNAJA3 MUTATION ANALYSIS"
[1] 3
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               3              781 
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               3              781 
[1] "NASP MUTATION ANALYSIS"
[1] 3
  NASP MUTATED NASP WILD-TYPE 
             5            779 
  NASP MUTATED NASP WILD-TYPE 
             5            779 
[1] "SLC23A1 MUTATION ANALYSIS"
[1] 3
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                6               778 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                6               778 
[1] "RILPL1 MUTATION ANALYSIS"
[1] 3
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               5              779 
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               5              779 
[1] "NIPBL MUTATION ANALYSIS"
[1] 3
  NIPBL MUTATED NIPBL WILD-TYPE 
             15             769 
  NIPBL MUTATED NIPBL WILD-TYPE 
             15             769 
[1] "FAM47A MUTATION ANALYSIS"
[1] 3
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              778 
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              778 
[1] "RHEB MUTATION ANALYSIS"
[1] 3
  RHEB MUTATED RHEB WILD-TYPE 
             3            781 
  RHEB MUTATED RHEB WILD-TYPE 
             3            781 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             5            779 
  BRAF MUTATED BRAF WILD-TYPE 
             5            779 
[1] "MLL3 MUTATION ANALYSIS"
[1] 3
  MLL3 MUTATED MLL3 WILD-TYPE 
            42            742 
  MLL3 MUTATED MLL3 WILD-TYPE 
            42            742 
[1] "ANK3 MUTATION ANALYSIS"
[1] 3
  ANK3 MUTATED ANK3 WILD-TYPE 
            22            762 
  ANK3 MUTATED ANK3 WILD-TYPE 
            22            762 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            780 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            780 
[1] "LHX1 MUTATION ANALYSIS"
[1] 3
  LHX1 MUTATED LHX1 WILD-TYPE 
             4            780 
  LHX1 MUTATED LHX1 WILD-TYPE 
             4            780 
[1] "SCARB2 MUTATION ANALYSIS"
[1] 3
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               4              780 
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               4              780 
[1] "C1ORF25 MUTATION ANALYSIS"
[1] 3
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                6               778 
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                6               778 
[1] "KDELR3 MUTATION ANALYSIS"
[1] 3
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               7              777 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               7              777 
[1] "TTLL6 MUTATION ANALYSIS"
[1] 3
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              4             780 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              4             780 
[1] "STXBP3 MUTATION ANALYSIS"
[1] 3
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               5              779 
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               5              779 
[1] "FAM20C MUTATION ANALYSIS"
[1] 3
  FAM20C MUTATED FAM20C WILD-TYPE 
               5              779 
  FAM20C MUTATED FAM20C WILD-TYPE 
               5              779 
[1] "CCBL2 MUTATION ANALYSIS"
[1] 3
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              3             781 
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              3             781 
[1] "B3GNT6 MUTATION ANALYSIS"
[1] 3
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               3              781 
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               3              781 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              4             780 
  HNF1B MUTATED HNF1B WILD-TYPE 
              4             780 
[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 784 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=190,	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=528,	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=12,	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=26,	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   "360"   "2"    
freq.contrast "2"     "360"  
both >= 3     "FALSE" "FALSE"
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	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=41,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=37,	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 784 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 
423 111 237  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
423 111 237  11 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
423 111 237  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
423 111 237  11 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
293  40   5 
[1] "table(vv)"
vv
 N0  N1  N2 
293  40   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
293  40   5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
293  40   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=41, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=37, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    25  13
  TP53 WILD-TYPE 553 189
  TP53 MUTATED TP53 WILD-TYPE 
            38            742 
  TP53 MUTATED TP53 WILD-TYPE 
            13            189 
$`TP53 MUTATED`
TCGA-KL-8339 TCGA-CZ-4865 TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 
       28.11         5.46       153.73        90.48        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8341 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 
       44.84        86.56        24.79       129.37        25.91        65.19 
TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8403 
       52.27        19.33        11.21        59.08        42.35       105.47 
TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-AK-3440 
       10.68        16.67        99.88       105.60        90.48        94.19 
TCGA-B0-4710 TCGA-B0-5098 TCGA-B0-5117 TCGA-BP-4176 TCGA-BP-4770 TCGA-CJ-5677 
       57.70        52.08        52.87        64.27        10.82        25.71 
TCGA-CZ-5463 TCGA-5P-A9K3 TCGA-5P-A9KH TCGA-A4-A57E TCGA-B1-A655 TCGA-B3-4104 
       21.76        15.48        67.43         8.48        16.77        34.49 
TCGA-BQ-5881 TCGA-BQ-5893 
       47.80         7.92 

$`TP53 WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3358 
      102.81        23.28        28.80        47.24       130.13        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
      107.54        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22       137.06       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       98.33        96.95        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 
       51.06        31.33        23.47        87.91        25.48       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 
        3.55         0.99        87.12         2.50       115.00       100.87 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 
      100.47       103.40        92.71       104.55       103.10        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
       68.61       109.51        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       13.15         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      133.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 
       62.93        43.04        12.99        12.39        27.09        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       36.49        20.25        20.32        33.83        29.03        30.58 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         7.66         0.95         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  TP53 MUTATED TP53 WILD-TYPE 
          5.46           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        153.73         194.79 
  TP53 MUTATED TP53 WILD-TYPE 
         46.32          36.90 
[1] "5.5 - 153.7 (46.3)" "0.1 - 194.8 (36.9)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED        12       10         6        8
  TP53 WILD-TYPE     387       79       169       85
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             12            387
  STAGE II            10             79
  STAGE III            6            169
  STAGE IV             8             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
  TP53 MUTATED    13  12  11   2
  TP53 WILD-TYPE 410  99 226   9
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           13            410
  T2           12             99
  T3           11            226
  T4            2              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
  TP53 MUTATED    15   3   2
  TP53 WILD-TYPE 278  37   3
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           15            278
  N1            3             37
  N2            2              3
[1] 3 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
  TP53 MUTATED    21   4
  TP53 WILD-TYPE 473  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     21    4
  TP53 WILD-TYPE  473   77
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           21            473
  1            4             77
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    15  23
  TP53 WILD-TYPE 243 503
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     15   23
  TP53 WILD-TYPE  243  503
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           15            243
  MALE             23            503
[1] 2 2
[1] FALSE
D1V8, 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                                       7
  TP53 WILD-TYPE                                   275
D1V9, multiclass
                                       clus
vv                                      TP53 MUTATED TP53 WILD-TYPE
  KIDNEY CHROMOPHOBE                              22             44
  KIDNEY CLEAR CELL RENAL CARCINOMA                9            427
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            7            275
[1] 3 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
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     2
  TP53 WILD-TYPE                                2    12
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           2    33
  TP53 WILD-TYPE                        81   630
D1V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2             12
  BLACK OR AFRICAN AMERICAN                   2             81
  WHITE                                      33            630
[1] 4 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
  TP53 MUTATED     1  23
  TP53 WILD-TYPE  35 532
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   23
  TP53 WILD-TYPE   35  532
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           23            532
[1] 2 2
[1] FALSE

Clustering(2) Variable = PTEN MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    20   8
  PTEN WILD-TYPE 558 194
  PTEN MUTATED PTEN WILD-TYPE 
            28            752 
  PTEN MUTATED PTEN WILD-TYPE 
             8            194 
$`PTEN MUTATED`
TCGA-B8-4621 TCGA-BP-5199 TCGA-DV-5568 TCGA-B1-A657 TCGA-PJ-A8JU TCGA-KL-8323 
       25.91        44.55        12.16        21.07        12.49        38.07 
TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 TCGA-AK-3427 
       90.48        30.25        54.74        16.67        96.62       117.80 
TCGA-B0-4694 TCGA-B0-4810 TCGA-B0-4843 TCGA-B8-5158 TCGA-BP-4161 TCGA-BP-4326 
        3.48        15.72        10.52        40.04        90.28        53.42 
TCGA-BP-4345 TCGA-BP-4351 TCGA-BP-5010 TCGA-CJ-4871 TCGA-EU-5907 TCGA-A4-7996 
       49.84        31.89        28.87        79.66         4.18        16.64 
TCGA-BQ-7051 TCGA-P4-A5E7 TCGA-UZ-A9Q1 TCGA-Y8-A897 
       50.40        87.09        51.35        18.05 

$`PTEN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4158 
       70.68       119.38       126.05        24.82         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.79        31.27        63.25        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
        5.46        43.69        45.96        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       23.90        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B3-A6W5 
       12.99        76.64        49.25        21.67        27.68        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
       15.62         6.74       153.73        23.84       109.22       137.06 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8416 
       92.71       104.55       103.10        99.88       105.60        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       20.28       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        1.41         4.57         2.53        19.00        65.10         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       85.51       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.02        37.48        35.21         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        6.77         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
        2.76       123.62        48.26        93.34        61.28        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       20.25        17.62        31.13        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.64        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  PTEN MUTATED PTEN WILD-TYPE 
          3.48           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
        117.80         194.79 
  PTEN MUTATED PTEN WILD-TYPE 
        34.980         36.985 
[1] "3.5 - 117.8 (35.0)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.1"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED        13        2        11        2
  PTEN WILD-TYPE     386       87       164       91
D2V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I             13            386
  STAGE II             2             87
  STAGE III           11            164
  STAGE IV             2             91
[1] 4 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    13   2  13   0
  PTEN WILD-TYPE 410 109 224  11
D2V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1           13            410
  T2            2            109
  T3           13            224
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PTEN MUTATED    14   3   1
  PTEN WILD-TYPE 279  37   4
D2V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           14            279
  N1            3             37
  N2            1              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
  PTEN MUTATED    21   1
  PTEN WILD-TYPE 473  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     21    1
  PTEN WILD-TYPE  473   80
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           21            473
  1            1             80
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  PTEN MUTATED    11  17
  PTEN WILD-TYPE 247 509
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     11   17
  PTEN WILD-TYPE  247  509
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE           11            247
  MALE             17            509
[1] 2 2
[1] FALSE
D2V8, 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                                       7
  PTEN WILD-TYPE                                   275
D2V9, multiclass
                                       clus
vv                                      PTEN MUTATED PTEN WILD-TYPE
  KIDNEY CHROMOPHOBE                               6             60
  KIDNEY CLEAR CELL RENAL CARCINOMA               15            421
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            7            275
[1] 3 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
  PTEN MUTATED                                  0     1
  PTEN WILD-TYPE                                2    13
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           1    26
  PTEN WILD-TYPE                        82   637
D2V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             13
  BLACK OR AFRICAN AMERICAN                   1             82
  WHITE                                      26            637
[1] 4 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
  PTEN MUTATED     1  19
  PTEN WILD-TYPE  35 536
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   19
  PTEN WILD-TYPE   35  536
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           19            536
[1] 2 2
[1] FALSE

Clustering(3) Variable = SETD2 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    38  23
  SETD2 WILD-TYPE 540 179
  SETD2 MUTATED SETD2 WILD-TYPE 
             61             719 
  SETD2 MUTATED SETD2 WILD-TYPE 
             23             179 
$`SETD2 MUTATED`
TCGA-A3-3358 TCGA-AK-3455 TCGA-B0-4712 TCGA-BP-5006 TCGA-BP-5178 TCGA-CJ-4891 
       42.97        22.45        43.96        27.62        62.86        26.93 
TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-B9-A44B TCGA-KL-8337 
       33.07        12.26        12.99        21.86        11.87        44.84 
TCGA-KM-8438 TCGA-A3-3311 TCGA-A3-3367 TCGA-AK-3431 TCGA-B0-4710 TCGA-B0-4718 
      151.96        39.16        74.63        73.68        57.70        58.45 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4837 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5098 
       46.59         5.52        45.30        36.85        11.90        52.08 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5699 TCGA-B2-4101 TCGA-B4-5835 
       48.82        46.39        42.41       126.28        21.30         0.53 
TCGA-B8-4622 TCGA-BP-4161 TCGA-BP-4329 TCGA-BP-4343 TCGA-BP-4774 TCGA-BP-4790 
       50.14        90.28        27.78        62.86        61.97        36.53 
TCGA-BP-4983 TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5678 
       46.45         6.35        19.82       131.08       133.71        18.87 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5580 TCGA-CW-5591 TCGA-CZ-4861 TCGA-CZ-5459 
      122.83        73.35        64.57        74.66        14.66        55.33 
TCGA-CZ-5461 TCGA-CZ-5470 TCGA-4A-A93X TCGA-5P-A9K3 TCGA-A4-8098 TCGA-B1-A656 
       10.85        12.69        12.82        15.48        29.46        20.32 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7061 TCGA-GL-A9DE 
       86.76         8.88         7.66         0.95         7.17        16.31 
TCGA-SX-A7SM 
       11.93 

$`SETD2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 
      109.91        58.49        28.73        19.73        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
       24.82        25.91         1.18       111.02        94.72        32.61 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       80.68        74.17        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5009 TCGA-BP-5168 
       27.22         5.82        45.07        41.62        35.90        48.10 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       25.58        16.18        22.49        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       10.16        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       96.95        92.55        30.25        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 
       73.91        71.41        28.80        54.74        62.37        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       45.53        88.37        51.25        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       15.78        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       19.00        65.10         5.98         2.14         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
       15.72         0.59        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-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5696 
       52.87        51.02        38.43        56.98       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5641 
       32.61        35.90         1.68        31.96        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
       12.00         5.10         1.25         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       45.37        17.19        25.55        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 
        0.53        34.39        14.30        85.51       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-4330 TCGA-BP-4337 
       61.78        64.27        54.90        53.42        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       13.15        10.82         5.33        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       48.95        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 
       38.70        37.02        37.48        35.21        28.87        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5200 
       33.24        23.47        13.41        24.62        33.47        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 
       67.00        53.42        62.66       119.64         7.36        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6090 
       81.83        85.78        66.31        78.18         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
       18.77        25.45        47.08        69.21        58.75        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        90.54        91.69        94.45        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       84.30        22.52         2.40         1.94        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K8 
       49.58        90.21        22.26        78.64        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       10.82         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       61.28        50.40        49.84         7.63         7.04         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
       27.65         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.53            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
         151.96          194.79 
  SETD2 MUTATED SETD2 WILD-TYPE 
          36.85           37.02 
[1] "0.5 - 152.0 (36.9)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.6"
D3V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        20        7        20       13
  SETD2 WILD-TYPE     379       82       155       80
D3V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              20             379
  STAGE II              7              82
  STAGE III            20             155
  STAGE IV             13              80
[1] 4 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    22   9  28   2
  SETD2 WILD-TYPE 401 102 209   9
D3V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            22             401
  T2             9             102
  T3            28             209
  T4             2               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
  SETD2 MUTATED    28   4   0
  SETD2 WILD-TYPE 265  36   5
D3V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            28             265
  N1             4              36
  N2             0               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
  SETD2 MUTATED    41  11
  SETD2 WILD-TYPE 453  70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     41   11
  SETD2 WILD-TYPE  453   70
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            41             453
  1            11              70
[1] 2 2
[1] FALSE
D3V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    17  44
  SETD2 WILD-TYPE 241 482
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     17   44
  SETD2 WILD-TYPE  241  482
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            17             241
  MALE              44             482
[1] 2 2
[1] FALSE
D3V8, 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                                      16
  SETD2 WILD-TYPE                                   266
D3V9, multiclass
                                       clus
vv                                      SETD2 MUTATED SETD2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                43             393
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            16             266
[1] 3 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
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      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-B9-4117 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     1
  SETD2 WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           9    49
  SETD2 WILD-TYPE                        74   614
D3V12, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    9              74
  WHITE                                       49             614
[1] 4 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
  SETD2 MUTATED     1  43
  SETD2 WILD-TYPE  35 512
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   43
  SETD2 WILD-TYPE   35  512
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              35
  NOT HISPANIC OR LATINO            43             512
[1] 2 2
[1] FALSE

Clustering(4) Variable = PBRM1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    93  49
  PBRM1 WILD-TYPE 485 153
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            142             638 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             49             153 
$`PBRM1 MUTATED`
TCGA-AK-3425 TCGA-B0-4815 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
      109.91        52.21       133.94        15.78        70.68       119.38 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
      111.02        32.61        27.22         5.82        45.07        41.62 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       48.10        49.15        27.02        75.58       103.43        46.16 
TCGA-DV-5566 TCGA-5P-A9JU TCGA-B9-A44B TCGA-BQ-7058 TCGA-IA-A83W TCGA-A3-3311 
       45.96        12.26        11.87        11.28        67.17        39.16 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3362 TCGA-A3-3367 
       48.59        36.36        37.38        48.82        51.25        74.63 
TCGA-A3-3373 TCGA-A3-3387 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3458 
       53.29        20.28        73.68        68.61       109.51        38.40 
TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4828 
       82.45         2.14        58.45        45.07        16.77        10.09 
TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5094 
       56.68        26.07         2.27        36.85        25.32        10.95 
TCGA-B0-5096 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
        2.24        90.48        30.48        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5703 
       41.88        38.43        46.39        85.78       126.28        73.84 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4099 
      149.16        79.89       131.15        89.49        91.46        31.96 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4154 
       12.00         5.10         4.64         0.23        49.97        45.37 
TCGA-B8-5158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4337 
       40.04        85.51        90.28        64.27        27.78         0.07 
TCGA-BP-4341 TCGA-BP-4774 TCGA-BP-4801 TCGA-BP-4960 TCGA-BP-4964 TCGA-BP-4973 
       52.24        61.97        36.95        71.41        61.22        45.50 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       47.11        36.07        33.34        31.30        36.95         3.88 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        6.35        79.30        74.40        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4644 
       13.35        19.82        34.95       115.00        46.55        11.05 
TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4903 TCGA-CJ-4905 
       79.66       116.84        30.64        51.52        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5676 
       50.33        54.48        38.56         4.57        18.81       133.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6033 TCGA-CW-5580 
       18.87        22.32       122.83        73.35         7.36        64.57 
TCGA-CW-5589 TCGA-CZ-4853 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       78.18        25.45        79.53        23.74        18.44        79.63 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
       94.45        10.85        84.30        22.52        12.69        80.19 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-EU-5907 TCGA-4A-A93X TCGA-5P-A9K3 TCGA-A4-7583 
       12.26        62.63         4.18        12.82        15.48         0.10 
TCGA-BQ-5890 TCGA-BQ-7061 TCGA-GL-A9DE TCGA-UZ-A9PJ 
        7.66         7.17        16.31        26.20 

$`PBRM1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
       42.97        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       18.51       112.80       126.05        24.82        25.91         1.18 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       94.72        80.68        74.17        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5199 
       25.81        27.62        35.90        62.86        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 
       31.27        63.25        26.93        27.65       108.56       118.85 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5569 
        0.59       107.54         5.46        43.69        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       25.58        16.18        22.49        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 
       11.97        96.92        44.84        26.27        20.12        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU 
       16.34        12.13        29.26        19.73        17.75        12.49 
TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       35.38        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       92.55        24.16        49.02        52.93        45.53        88.37 
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 
       74.76        43.20        55.76        65.52       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
      109.41        15.78        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       83.21        37.58        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       57.70         6.64         3.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
        5.52        33.50         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4848 
        6.71        10.52        10.29        65.29        39.45        29.03 
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-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
        7.30        15.09         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5117 
       62.89        90.87        52.54        58.59        19.30        52.87 
TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5697 
       51.02        48.82        56.98        42.41       129.67        86.47 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B2-3923 
       80.91        71.41       105.37       123.09       130.65        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5834 
       35.90         1.68        21.30        31.66        21.57         1.25 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 
        0.53         5.46         0.36        23.31        16.80        42.71 
TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
       25.05        17.19        25.55        50.14        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        0.53        34.39        14.30       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 
       54.90        53.42        62.07        93.99        18.48        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       10.98         6.71        47.97        63.62        58.68        60.30 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
        6.74        57.40        14.24        48.89        49.38         6.94 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       14.93        46.45        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 
        2.04        74.20        30.64        52.27         9.63        38.30 
TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       37.22        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5202 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
        0.95        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        47.18        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-4892 TCGA-CJ-4893 
      113.46        64.18        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       49.28        45.14         3.06       131.08        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6028 
       25.71        25.25        18.15        62.10        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
       62.66       119.64        92.02        81.83        85.78        66.31 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 
       74.66         1.35        83.90        18.77        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5467 
       90.54        91.69        55.33        10.22        21.76         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 
        1.94        31.10        67.96        65.65        14.63        22.78 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       18.12         3.91         6.77         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       90.21        22.26        78.64        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7585 
       12.39        27.09        67.43        18.21        19.63        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35        10.82         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.63         7.04         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.13 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         149.16          194.79 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         43.755          34.670 
[1] "0.1 - 149.2 (43.8)" "0.1 - 194.8 (34.7)"
[1] "hr=" "1.3"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        71       12        36       23
  PBRM1 WILD-TYPE     328       77       139       70
D4V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              71             328
  STAGE II             12              77
  STAGE III            36             139
  STAGE IV             23              70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  PBRM1 MUTATED    72  20  51   0
  PBRM1 WILD-TYPE 351  91 186  11
D4V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            72             351
  T2            20              91
  T3            51             186
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PBRM1 MUTATED    64   3   0
  PBRM1 WILD-TYPE 229  37   5
D4V5, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  N0            64             229
  N1             3              37
  N2             0               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"
D4V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   115  22
  PBRM1 WILD-TYPE 379  59
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    115   22
  PBRM1 WILD-TYPE  379   59
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0           115             379
  1            22              59
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    45  98
  PBRM1 WILD-TYPE 213 428
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     45   98
  PBRM1 WILD-TYPE  213  428
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            45             213
  MALE              98             428
[1] 2 2
[1] FALSE
D4V8, 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                                      11
  PBRM1 WILD-TYPE                                   271
D4V9, multiclass
                                       clus
vv                                      PBRM1 MUTATED PBRM1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA               131             305
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            11             271
[1] 3 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
D4V11, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     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-2Z-A9J3 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      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-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     1
  PBRM1 WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           6   132
  PBRM1 WILD-TYPE                        77   531
D4V12, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    6              77
  WHITE                                      132             531
[1] 4 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
  PBRM1 MUTATED     5  96
  PBRM1 WILD-TYPE  31 459
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      5   96
  PBRM1 WILD-TYPE   31  459
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 5              31
  NOT HISPANIC OR LATINO            96             459
[1] 2 2
[1] FALSE

Clustering(5) Variable = NEFH MUTATION ANALYSIS
D5V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    10   2
  NEFH WILD-TYPE 568 200
  NEFH MUTATED NEFH WILD-TYPE 
            12            768 
  NEFH MUTATED NEFH WILD-TYPE 
             2            200 
$`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-B9-A5W8 TCGA-HE-A5NL TCGA-KV-A74V TCGA-SX-A71V TCGA-SX-A7SL TCGA-UZ-A9PK 
       17.23        25.22        11.41        28.80        27.06       117.40 

$`NEFH WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3453 TCGA-AK-3456 
      109.51        94.19        46.78        78.64        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.55        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       25.25       122.83        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        22.06         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       49.45        44.61        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       26.47        53.10        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  NEFH MUTATED NEFH WILD-TYPE 
          2.14           0.07 
  NEFH MUTATED NEFH WILD-TYPE 
        117.40         194.79 
  NEFH MUTATED NEFH WILD-TYPE 
         27.93          37.12 
[1] "2.1 - 117.4 (27.9)" "0.1 - 194.8 (37.1)"
[1] "hr=" "1.6"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         6        3         1        2
  NEFH WILD-TYPE     393       86       174       91
D5V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              6            393
  STAGE II             3             86
  STAGE III            1            174
  STAGE IV             2             91
[1] 4 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     6   3   3   0
  NEFH WILD-TYPE 417 108 234  11
D5V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            6            417
  T2            3            108
  T3            3            234
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NEFH MUTATED     4   0   0
  NEFH WILD-TYPE 289  40   5
D5V5, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  N0            4            289
  N1            0             40
  N2            0              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
  NEFH MUTATED     8   2
  NEFH WILD-TYPE 486  79
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      8    2
  NEFH WILD-TYPE  486   79
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            8            486
  1            2             79
[1] 2 2
[1] FALSE
D5V7, binary
                cls
clus               0   1
  NEFH MUTATED     1  11
  NEFH WILD-TYPE 257 515
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      1   11
  NEFH WILD-TYPE  257  515
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            1            257
  MALE             11            515
[1] 2 2
[1] FALSE
D5V8, 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                                       6
  NEFH WILD-TYPE                                   276
D5V9, multiclass
                                       clus
vv                                      NEFH MUTATED NEFH WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                6            430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            6            276
[1] 3 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:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             92 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164     TCGA-B8-5550 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     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-B9-4115     TCGA-B9-4117 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SR 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D5V11, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2             65 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    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-2Z-A9J3 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JN 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     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-B9-4117     TCGA-B9-A69E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SM     TCGA-SX-A7SR 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894     TCGA-Y8-A896 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Y8-A8RY 
"NEFH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           1     9
  NEFH WILD-TYPE                        82   654
D5V12, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   1             82
  WHITE                                       9            654
[1] 4 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
  NEFH MUTATED     0   9
  NEFH WILD-TYPE  36 546
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    9
  NEFH WILD-TYPE   36  546
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            9            546
[1] 2 2
[1] FALSE

Clustering(6) Variable = VHL MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  VHL MUTATED   127  69
  VHL WILD-TYPE 451 133
  VHL MUTATED VHL WILD-TYPE 
          196           584 
  VHL MUTATED VHL WILD-TYPE 
           69           133 
$`VHL MUTATED`
TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       58.49        22.45        43.96        18.51       112.80       133.94 
TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4164 TCGA-BP-4342 
       70.68       126.05        24.82         1.18        32.61        74.17 
TCGA-BP-4762 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       44.15         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5181 TCGA-BP-5199 
       45.07        41.62        27.62        35.90        49.15        44.55 
TCGA-CJ-4636 TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
       63.25        27.65       118.85        75.58       103.43         0.59 
TCGA-BQ-5892 TCGA-KN-8432 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 
       11.97         2.50        48.82        45.53        51.25        53.29 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3445 TCGA-AK-3458 TCGA-B0-4690 TCGA-B0-4700 
       55.76        65.52        78.64        38.40         1.41        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4814 
        5.98         2.14         6.64         3.25        15.72         5.52 
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-B0-4842 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4852 
       10.09        78.44        56.68        65.29        26.07        36.85 
TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5095 TCGA-B0-5096 
       70.52        43.30        11.90        25.32         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       21.86        15.95        90.87        52.54        30.48        58.59 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5703 
       38.63        52.73        42.41       129.67        85.78        73.84 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3924 
      149.16       130.65        79.89       131.15        91.46        35.90 
TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        5.10         4.64         0.36        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 
       45.37        23.74        27.02        24.23         6.38         0.53 
TCGA-BP-4159 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4340 TCGA-BP-4341 
       85.51         0.43        89.36        27.78        18.48        52.24 
TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       12.23        31.33        72.59        77.98        41.75        71.80 
TCGA-BP-4771 TCGA-BP-4789 TCGA-BP-4798 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
        5.33        48.95        10.98        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4975 
       61.22         6.74        57.40        14.24         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 
       14.93        33.34         3.88        46.45        16.47        30.64 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
       38.70        37.02        37.48        35.21         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       42.44        37.25        22.78        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 
       24.62        33.47        19.82       115.00        73.22        14.17 
TCGA-CJ-4644 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4892 
       11.05        47.18       116.84        57.83       113.46        50.01 
TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 
       56.35        51.29        50.33        54.48        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 
        4.57       133.71        25.71        25.25        73.35        67.00 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5588 
       62.66       119.64         7.36        64.57        81.83        66.31 
TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-5458 
       74.66        83.90        25.45        69.21        14.66        91.69 
TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       94.45        84.30        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       65.65        12.26        14.63        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-AL-3473 TCGA-WN-A9G9 
        6.77         4.18        62.66        26.01 

$`VHL WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5694 
       42.97       109.91        28.73        19.73        52.21        15.78 
TCGA-B0-5698 TCGA-B8-4621 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4760 
      119.38        25.91       111.02        94.72        80.68        77.62 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4993 TCGA-BP-5168 
       60.59        11.64        20.38        37.25         5.82        48.10 
TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4891 TCGA-CJ-4904 
       62.86        27.02        31.79        31.27        26.93       108.56 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       46.16       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        13.25        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        0.99        52.27        87.12        19.33        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       74.63        74.76        43.20        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       46.78        94.29        83.21        37.58        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       12.13        40.70         4.57         2.53         3.48        19.00 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 
       57.70        58.45        46.59         0.59        45.07        33.50 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 
       40.70        45.30        27.42        53.88         6.71        10.52 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5080 
       10.29        39.45        29.03         2.27        20.94        11.24 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5100 
       34.36         7.30        15.09        10.95        52.08        62.89 
TCGA-B0-5104 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       90.48        19.30        66.05        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5697 TCGA-B0-5699 
       38.43        48.82        46.39        56.98        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5712 TCGA-B2-3923 
       80.91        71.41       105.37       123.09        89.49        32.61 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         5.46         0.23        23.31        16.80 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5545 
       17.19        25.55        50.14        40.04         0.85        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4161 TCGA-BP-4162 
       16.60        48.53        34.39        14.30        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       93.34        99.85        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       64.27        54.90        53.42        62.07         0.07        93.99 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.84        49.08        44.94        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       33.99        12.30         5.98        48.07        13.15        10.82 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 
       61.97        56.91        68.38        15.78        36.53        36.39 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-4972 
       36.95         6.71        47.97        58.68        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4994 
       45.50        36.07        46.45        31.30        36.95        43.00 
TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5200 
       18.51        28.87        38.30        37.22        13.35        34.95 
TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
        0.95        46.55       106.16       114.41        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        79.66        74.27        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 
       64.27        71.87        66.21        61.91        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       51.52        63.98       115.69        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4913 
       50.24        47.67        49.97        49.18        49.28        38.56 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       18.81       131.08        72.00       129.40        18.87        22.32 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5585 
       18.15       122.83        62.10        53.42        92.02        85.78 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4863 
       78.18         1.35        18.77        47.08        58.75        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        90.54        55.33        10.85        10.22        21.76 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5988 TCGA-2K-A9WE TCGA-2Z-A9J1 
       22.52         2.40         1.94        22.78         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  VHL MUTATED VHL WILD-TYPE 
         0.36          0.07 
  VHL MUTATED VHL WILD-TYPE 
       149.16        194.79 
  VHL MUTATED VHL WILD-TYPE 
       41.685        36.000 
[1] "0.4 - 149.2 (41.7)" "0.1 - 194.8 (36.0)"
[1] "hr=" "1.5"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED       104       18        44       29
  VHL WILD-TYPE     295       71       131       64
D6V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I           104           295
  STAGE II           18            71
  STAGE III          44           131
  STAGE IV           29            64
[1] 4 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   105  22  64   5
  VHL WILD-TYPE 318  89 173   6
D6V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1         105           318
  T2          22            89
  T3          64           173
  T4           5             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  VHL MUTATED    87   5   0
  VHL WILD-TYPE 206  35   5
D6V5, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  N0          87           206
  N1           5            35
  N2           0             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
  VHL MUTATED   165  29
  VHL WILD-TYPE 329  52
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    165   29
  VHL WILD-TYPE  329   52
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0         165           329
  1          29            52
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus              0   1
  VHL MUTATED    74 122
  VHL WILD-TYPE 184 404
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     74  122
  VHL WILD-TYPE  184  404
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          74           184
  MALE           122           404
[1] 2 2
[1] FALSE
D6V8, 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                                       3
  VHL WILD-TYPE                                   279
D6V9, multiclass
                                       clus
vv                                      VHL MUTATED VHL WILD-TYPE
  KIDNEY CHROMOPHOBE                              1            65
  KIDNEY CLEAR CELL RENAL CARCINOMA             192           244
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           3           279
[1] 3 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:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            2            92 
   TCGA-B8-4621    TCGA-2Z-A9JD    TCGA-2Z-A9JQ    TCGA-5P-A9JU    TCGA-B9-A44B 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-GL-A59T    TCGA-IZ-A6M8 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-PJ-A5Z9    TCGA-PJ-A8JU    TCGA-SX-A71W    TCGA-UZ-A9PO    TCGA-UZ-A9PR 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-Y8-A8RZ    TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KO-8409    TCGA-KO-8416    TCGA-AK-3451    TCGA-B8-4146    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-2Z-A9J2    TCGA-2Z-A9J5    TCGA-2Z-A9J7 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JK    TCGA-2Z-A9JM    TCGA-2Z-A9JN 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-2Z-A9JO    TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-5P-A9K3    TCGA-5P-A9KE 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G 
"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-G7-A8LB 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-7773    TCGA-GL-A9DD    TCGA-HE-A5NI 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U    TCGA-IA-A83S    TCGA-IA-A83V 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-MH-A854    TCGA-MH-A856    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-Q2-A5QZ 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SR 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-SX-A7SS    TCGA-UZ-A9PM    TCGA-UZ-A9PS    TCGA-UZ-A9PX    TCGA-Y8-A894 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-Y8-A896    TCGA-Y8-A8RY 
"VHL WILD-TYPE" "VHL WILD-TYPE" 
D6V11, continuous
[1] "Remove cluster labels:" "VHL MUTATED"           
clus
  VHL MUTATED VHL WILD-TYPE 
            2            65 
   TCGA-2Z-A9JD    TCGA-DW-5561    TCGA-PJ-A5Z9    TCGA-PJ-A8JU    TCGA-SX-A71W 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-UZ-A9PO    TCGA-UZ-A9PR    TCGA-Y8-A8RZ    TCGA-KL-8330    TCGA-KL-8335 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8433    TCGA-KO-8408 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-KO-8409    TCGA-AK-3451    TCGA-B8-5158    TCGA-B8-5550    TCGA-2Z-A9J3 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JN    TCGA-2Z-A9JO 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4117 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G    TCGA-G7-6793    TCGA-G7-6795 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-A8LB    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-7773 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-GL-A9DD    TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-MH-A854    TCGA-MH-A856 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-P4-A5E6    TCGA-Q2-A5QZ    TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A7SL 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-SX-A7SM    TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-UZ-A9PM    TCGA-UZ-A9PS 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
   TCGA-UZ-A9PX    TCGA-WN-AB4C    TCGA-Y8-A894    TCGA-Y8-A896    TCGA-Y8-A8RY 
"VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" "VHL WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VHL MUTATED                                  0     2
  VHL WILD-TYPE                                2    12
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED                           2   190
  VHL WILD-TYPE                        81   473
D6V12, multiclass
                                  clus
vv                                 VHL MUTATED VHL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      2            12
  BLACK OR AFRICAN AMERICAN                  2            81
  WHITE                                    190           473
[1] 4 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
  VHL MUTATED     8 125
  VHL WILD-TYPE  28 430
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      8  125
  VHL WILD-TYPE   28  430
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               8            28
  NOT HISPANIC OR LATINO         125           430
[1] 2 2
[1] FALSE

Clustering(7) Variable = NF2 MUTATION ANALYSIS
D7V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    11   5
  NF2 WILD-TYPE 567 197
  NF2 MUTATED NF2 WILD-TYPE 
           16           764 
  NF2 MUTATED NF2 WILD-TYPE 
            5           197 
$`NF2 MUTATED`
TCGA-BP-4986 TCGA-B1-A47M TCGA-B0-5084 TCGA-B0-5098 TCGA-B8-4153 TCGA-CJ-4638 
       25.81        21.67         7.30        52.08        25.05        14.17 
TCGA-CJ-4901 TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-EV-5902 TCGA-G7-6797 
       47.67         0.46        86.76         8.88        19.00        25.15 
TCGA-GL-7966 TCGA-P4-A5EA TCGA-SX-A7SL TCGA-Y8-A896 
        3.68         6.61        27.06        18.64 

$`NF2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       61.51        53.65        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47O 
       21.37         0.89        12.99        76.64        49.25        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        34.36        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       42.71        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       46.55        73.22       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       50.24        56.35        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
       42.94        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        49.45        44.61        28.80        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  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        37.365 
[1] "0.5 - 86.8 (20.3)"  "0.1 - 194.8 (37.4)"
[1] "hr=" "2.2"
D7V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         4        0         8        3
  NF2 WILD-TYPE     395       89       167       90
D7V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             4           395
  STAGE II            0            89
  STAGE III           8           167
  STAGE IV            3            90
[1] 4 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 418 110 227  11
D7V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           5           418
  T2           1           110
  T3          10           227
  T4           0            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NF2 MUTATED     1   5   0
  NF2 WILD-TYPE 292  35   5
D7V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           1           292
  N1           5            35
  N2           0             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"
D7V6, binary
               cls
clus              0   1
  NF2 MUTATED     7   3
  NF2 WILD-TYPE 487  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      7    3
  NF2 WILD-TYPE  487   78
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           7           487
  1           3            78
[1] 2 2
[1] FALSE
D7V7, binary
               cls
clus              0   1
  NF2 MUTATED     6  10
  NF2 WILD-TYPE 252 516
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      6   10
  NF2 WILD-TYPE  252  516
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           6           252
  MALE            10           516
[1] 2 2
[1] FALSE
D7V8, 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                                   272
D7V9, 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           272
[1] 3 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
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2    14
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           4    11
  NF2 WILD-TYPE                        79   652
D7V12, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            14
  BLACK OR AFRICAN AMERICAN                  4            79
  WHITE                                     11           652
[1] 4 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
  NF2 MUTATED     1  11
  NF2 WILD-TYPE  35 544
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      1   11
  NF2 WILD-TYPE   35  544
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               1            35
  NOT HISPANIC OR LATINO          11           544
[1] 2 2
[1] FALSE

Clustering(8) Variable = MET MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  MET MUTATED    20   5
  MET WILD-TYPE 558 197
  MET MUTATED MET WILD-TYPE 
           25           755 
  MET MUTATED MET WILD-TYPE 
            5           197 
$`MET MUTATED`
TCGA-A4-7734 TCGA-IA-A83W TCGA-B0-5098 TCGA-B0-5707 TCGA-CW-6087 TCGA-EU-5907 
        0.89        67.17        52.08       123.09         1.35         4.18 
TCGA-4A-A93W TCGA-5P-A9KA TCGA-A4-7997 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-7332 
        0.13        12.99        30.48        66.71        67.73        37.51 
TCGA-BQ-5882 TCGA-BQ-7059 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-G7-A8LE TCGA-GL-A59R 
       21.63         7.63        80.88        74.60        80.65        12.43 
TCGA-HE-A5NH TCGA-IA-A40U TCGA-IZ-8196 TCGA-MH-A561 TCGA-SX-A71S TCGA-SX-A7SQ 
       26.01        16.80        21.34        27.65        49.45        41.62 
TCGA-UZ-A9PJ 
       26.20 

$`MET WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       61.02        17.95        84.89        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6097 
       85.78        66.31        78.18        74.66        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93X 
       30.71        24.33        31.20        29.36         5.29        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       15.48        62.93        43.04        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       70.19        62.66         2.20        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        79.86        51.19 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        16.90       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
       27.65         1.05        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
       58.19        11.84        56.75        73.25        25.22        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-A6M9 
        2.04        85.78        88.24        96.69        22.26        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       34.29        27.78        30.38        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71U 
       92.58        16.01        50.60        14.07        47.90        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR 
       28.80        27.06        11.93        19.00        16.31        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        18.02       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  MET MUTATED MET WILD-TYPE 
         0.13          0.07 
  MET MUTATED MET WILD-TYPE 
       123.09        194.79 
  MET MUTATED MET WILD-TYPE 
        27.65         37.22 
[1] "0.1 - 123.1 (27.6)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.1"
D8V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED        16        1         4        2
  MET WILD-TYPE     383       88       171       91
D8V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I            16           383
  STAGE II            1            88
  STAGE III           4           171
  STAGE IV            2            91
[1] 4 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    17   2   6   0
  MET WILD-TYPE 406 109 231  11
D8V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1          17           406
  T2           2           109
  T3           6           231
  T4           0            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MET MUTATED     7   1   1
  MET WILD-TYPE 286  39   4
D8V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0           7           286
  N1           1            39
  N2           1             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"
D8V6, binary
               cls
clus              0   1
  MET MUTATED    12   1
  MET WILD-TYPE 482  80
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED     12    1
  MET WILD-TYPE  482   80
   clus
vv  MET MUTATED MET WILD-TYPE
  0          12           482
  1           1            80
[1] 2 2
[1] FALSE
D8V7, binary
               cls
clus              0   1
  MET MUTATED     7  18
  MET WILD-TYPE 251 508
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      7   18
  MET WILD-TYPE  251  508
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           7           251
  MALE            18           508
[1] 2 2
[1] FALSE
D8V8, continuous
               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                                      21
  MET WILD-TYPE                                   261
D8V9, multiclass
                                       clus
vv                                      MET MUTATED MET WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               4           432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA          21           261
[1] 3 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
D8V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2    14
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           3    18
  MET WILD-TYPE                        80   645
D8V12, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            14
  BLACK OR AFRICAN AMERICAN                  3            80
  WHITE                                     18           645
[1] 4 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
  MET MUTATED     1  20
  MET WILD-TYPE  35 535
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   20
  MET WILD-TYPE   35  535
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1            35
  NOT HISPANIC OR LATINO          20           535
[1] 2 2
[1] FALSE

Clustering(9) Variable = KDM5C MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    15  12
  KDM5C WILD-TYPE 563 190
  KDM5C MUTATED KDM5C WILD-TYPE 
             27             753 
  KDM5C MUTATED KDM5C WILD-TYPE 
             12             190 
$`KDM5C MUTATED`
TCGA-B0-5698 TCGA-BP-5189 TCGA-KL-8345 TCGA-A3-3331 TCGA-AK-3430 TCGA-AK-3458 
      119.38        27.02        54.74        48.82        15.78        38.40 
TCGA-B0-4694 TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4828 TCGA-B0-4837 TCGA-B0-4844 
        3.48        58.45        45.07        10.09        45.30        10.29 
TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5108 TCGA-B2-5641 TCGA-BP-4159 
       43.30        10.95        52.54        58.59        21.57        85.51 
TCGA-BP-4351 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5190 TCGA-BP-5202 TCGA-CJ-4871 
       31.89        18.51         6.35        33.24         0.95        79.66 
TCGA-CW-5581 TCGA-CZ-5467 TCGA-GL-A9DC 
       92.02         2.40        12.89 

$`KDM5C WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
       70.68       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 
       27.62        35.90        48.10        62.86        49.15        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       44.55        31.27        63.25        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       65.52        20.28       117.80       122.56       109.41        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        0.59         5.52        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 
       14.93        54.48        29.10        78.44        40.70        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        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-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       11.24        11.90        34.36         7.30        25.32        15.09 
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-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       90.87        90.48        30.48        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4161 
        6.38        48.53         0.53        34.39        14.30        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       62.86        49.84        49.08        44.94        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 
        3.88        46.45        16.47        43.00        30.64        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 
       37.02        37.48        35.21        28.87        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 
       42.44        37.25        37.22        22.78        13.35        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 
       13.41        24.62        33.47        19.82        34.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        49.25        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
        7.36        64.57        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
         119.38          194.79 
  KDM5C MUTATED KDM5C WILD-TYPE 
          33.24           37.02 
[1] "0.9 - 119.4 (33.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "2"  
D9V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        14        1         8        4
  KDM5C WILD-TYPE     385       88       167       89
D9V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              14             385
  STAGE II              1              88
  STAGE III             8             167
  STAGE IV              4              89
[1] 4 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    14   2  11   0
  KDM5C WILD-TYPE 409 109 226  11
D9V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            14             409
  T2             2             109
  T3            11             226
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM5C MUTATED    15   1   0
  KDM5C WILD-TYPE 278  39   5
D9V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            15             278
  N1             1              39
  N2             0               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
  KDM5C MUTATED    22   4
  KDM5C WILD-TYPE 472  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     22    4
  KDM5C WILD-TYPE  472   77
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            22             472
  1             4              77
[1] 2 2
[1] FALSE
D9V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     4  23
  KDM5C WILD-TYPE 254 503
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      4   23
  KDM5C WILD-TYPE  254  503
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             4             254
  MALE              23             503
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7836      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A7SO      TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861      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-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0 
"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-G7-A8LB      TCGA-G7-A8LC 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      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      TCGA-SX-A71R 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-V9-A7HT 
"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                                       1
  KDM5C WILD-TYPE                                   281
D9V9, multiclass
                                       clus
vv                                      KDM5C MUTATED KDM5C WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                25             411
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             281
[1] 3 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
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              93 
     TCGA-B8-4621      TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B9-A44B      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-GL-A59T      TCGA-IZ-A6M8      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     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-B8-5158      TCGA-B8-5164      TCGA-B8-5550 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-2Z-A9J2      TCGA-2Z-A9J5      TCGA-2Z-A9J7      TCGA-2Z-A9J8 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-2Z-A9JI      TCGA-2Z-A9JK      TCGA-2Z-A9JM      TCGA-2Z-A9JN 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-5P-A9K3 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-5P-A9KE      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-A69E      TCGA-DW-7963      TCGA-F9-A97G 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-GL-7773 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-GL-A9DD      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-IA-A83S      TCGA-IA-A83V      TCGA-MH-A854 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-MH-A856      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-Y8-A894      TCGA-Y8-A896 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-Y8-A8RY 
"KDM5C WILD-TYPE" 
D9V11, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     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-2Z-A9J3 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      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-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5C MUTATED                                  0     0
  KDM5C WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED                           1    26
  KDM5C WILD-TYPE                        82   637
D9V12, multiclass
                                  clus
vv                                 KDM5C MUTATED KDM5C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                       26             637
[1] 4 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
  KDM5C MUTATED     0  21
  KDM5C WILD-TYPE  36 534
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   21
  KDM5C WILD-TYPE   36  534
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO            21             534
[1] 2 2
[1] FALSE

Clustering(10) Variable = MTOR MUTATION ANALYSIS
D10V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    19  15
  MTOR WILD-TYPE 559 187
  MTOR MUTATED MTOR WILD-TYPE 
            34            746 
  MTOR MUTATED MTOR WILD-TYPE 
            15            187 
$`MTOR MUTATED`
TCGA-KM-8441 TCGA-B0-5691 TCGA-CJ-6027 TCGA-MH-A857 TCGA-KN-8437 TCGA-A3-3347 
       28.80       112.80       118.85        29.26       100.87        52.93 
TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5098 
      109.41        15.72        29.10        39.45        36.85        52.08 
TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5712 
       62.89        51.02        85.78        86.47        80.91        89.49 
TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-BP-5175 TCGA-BP-5176 TCGA-CJ-4644 
        5.10         4.64         0.23        30.64        52.27        11.05 
TCGA-CJ-4887 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 
       30.64        49.28        22.32        64.57        47.08       107.41 
TCGA-CZ-5987 TCGA-5P-A9KC TCGA-A4-7828 TCGA-BQ-7061 
       14.63        12.39         7.82         7.17 

$`MTOR WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3358 
      102.81        28.11        23.28        47.24       130.13        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       52.21        18.51       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 TCGA-BP-4160 
      126.05        24.82        25.91         1.18       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       32.61        80.68        74.17        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       44.55        31.27        63.25        26.93        27.65       108.56 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       23.90        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       84.89        67.17        16.34        12.13        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-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-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        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-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 
       37.38        48.82        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80       122.56        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       36.53        14.93        54.48        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        65.29        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        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-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
      126.28        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-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         5.46         0.36        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       74.20         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83       113.46        64.18        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97        51.29        49.18        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-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       53.42        62.66       119.64         7.36        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       18.77        25.45        69.21        58.75        14.66        63.39 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-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-5988 
       12.69        80.19        67.96        65.65        12.26        22.78 
TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH 
       15.48        62.93        43.04        12.99        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7915 
       18.21        19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  MTOR MUTATED MTOR WILD-TYPE 
          0.23           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        118.85         194.79 
  MTOR MUTATED MTOR WILD-TYPE 
        43.265         36.950 
[1] "0.2 - 118.8 (43.3)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.6"
D10V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED        14        3         9        7
  MTOR WILD-TYPE     385       86       166       86
D10V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I             14            385
  STAGE II             3             86
  STAGE III            9            166
  STAGE IV             7             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
  MTOR MUTATED    16   4  14   0
  MTOR WILD-TYPE 407 107 223  11
D10V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1           16            407
  T2            4            107
  T3           14            223
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTOR MUTATED    15   2   0
  MTOR WILD-TYPE 278  38   5
D10V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           15            278
  N1            2             38
  N2            0              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"
D10V6, binary
                cls
clus               0   1
  MTOR MUTATED    24   7
  MTOR WILD-TYPE 470  74
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     24    7
  MTOR WILD-TYPE  470   74
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           24            470
  1            7             74
[1] 2 2
[1] FALSE
D10V7, binary
                cls
clus               0   1
  MTOR MUTATED    19  15
  MTOR WILD-TYPE 239 511
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     19   15
  MTOR WILD-TYPE  239  511
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           19            239
  MALE             15            511
[1] 2 2
[1] FALSE
D10V8, 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                                       4
  MTOR WILD-TYPE                                   278
D10V9, multiclass
                                       clus
vv                                      MTOR MUTATED MTOR WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA               28            408
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            4            278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTOR MUTATED                                  0     0
  MTOR WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED                           5    29
  MTOR WILD-TYPE                        78   634
D10V12, multiclass
                                  clus
vv                                 MTOR MUTATED MTOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   5             78
  WHITE                                      29            634
[1] 4 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
  MTOR MUTATED     1  31
  MTOR WILD-TYPE  35 524
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   31
  MTOR WILD-TYPE   35  524
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           31            524
[1] 2 2
[1] FALSE

Clustering(11) Variable = ZNF814 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED    12   2
  ZNF814 WILD-TYPE 566 200
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              14              766 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2              200 
$`ZNF814 MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-DW-7840 TCGA-KL-8333 TCGA-KL-8344 TCGA-KO-8414 
       12.99        11.87         3.75        98.33        28.80       105.60 
TCGA-BP-5196 TCGA-CJ-5675 TCGA-2Z-A9J3 TCGA-5P-A9K8 TCGA-GL-A4EM TCGA-KV-A6GE 
       33.47       129.40        58.22        43.04         1.05        29.10 
TCGA-P4-A5EB TCGA-Y8-A894 
       99.12        18.64 

$`ZNF814 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 
       27.68        21.07        10.16        21.86        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       24.46        13.78        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 
       66.54        24.79        73.91        71.41        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        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-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      104.55       103.10        99.88        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       18.81       131.08        72.00       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       59.01       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68        27.65        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.09        18.41        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09        42.94         6.61        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A896 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            1.05             0.07 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          129.40           194.79 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
          31.285           37.120 
[1] "1.1 - 129.4 (31.3)" "0.1 - 194.8 (37.1)"
[1] "hr=" "1.9"
D11V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         6        4         3        0
  ZNF814 WILD-TYPE     393       85       172       93
D11V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                6              393
  STAGE II               4               85
  STAGE III              3              172
  STAGE IV               0               93
[1] 4 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   3   0
  ZNF814 WILD-TYPE 416 107 234  11
D11V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              7              416
  T2              4              107
  T3              3              234
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF814 MUTATED     3   1   0
  ZNF814 WILD-TYPE 290  39   5
D11V5, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  N0              3              290
  N1              1               39
  N2              0                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"
D11V6, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     5   0
  ZNF814 WILD-TYPE 489  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      5    0
  ZNF814 WILD-TYPE  489   81
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              5              489
  1              0               81
[1] 2 2
[1] FALSE
D11V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     3  11
  ZNF814 WILD-TYPE 255 515
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      3   11
  ZNF814 WILD-TYPE  255  515
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              3              255
  MALE               11              515
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440       TCGA-KM-8443 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639       TCGA-KN-8429 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428       TCGA-AK-3430 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-5456 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-5982       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-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       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       TCGA-SX-A71R 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-V9-A7HT 
"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                                       9
  ZNF814 WILD-TYPE                                   273
D11V9, multiclass
                                       clus
vv                                      ZNF814 MUTATED ZNF814 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 3               63
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              9              273
[1] 3 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
D11V11, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               65 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JN 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-A4-A48D 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A896 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Y8-A8RY 
"ZNF814 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           2    12
  ZNF814 WILD-TYPE                        81   651
D11V12, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     2               81
  WHITE                                        12              651
[1] 4 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
  ZNF814 MUTATED     0  11
  ZNF814 WILD-TYPE  36 544
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0   11
  ZNF814 WILD-TYPE   36  544
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO             11              544
[1] 2 2
[1] FALSE

Clustering(12) Variable = AR MUTATION ANALYSIS
D12V1, survival
              sevent
clus2            0   1
  AR MUTATED    12   3
  AR WILD-TYPE 566 199
  AR MUTATED AR WILD-TYPE 
          15          765 
  AR MUTATED AR WILD-TYPE 
           3          199 
$`AR MUTATED`
TCGA-KL-8344 TCGA-B8-5159 TCGA-2Z-A9J3 TCGA-2Z-A9JO TCGA-5P-A9JW TCGA-5P-A9JZ 
       28.80        23.74        58.22        31.20       106.55        90.21 
TCGA-A4-A5Y0 TCGA-B1-A656 TCGA-G7-A8LD TCGA-GL-A9DC TCGA-IA-A83T TCGA-SX-A71U 
        8.28        20.32        16.90        12.89        88.24        44.61 
TCGA-UZ-A9PL TCGA-UZ-A9Q1 TCGA-Y8-A8S0 
      103.63        51.35         6.02 

$`AR WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       73.91        71.41        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 
       17.19        25.55        50.14        40.04        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       59.01       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JP 
       54.64        51.52        38.99        30.71        24.33        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9K0 
        5.29         0.13        12.82        11.57        49.58        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        23.08        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD 
       12.92         3.68        27.65         1.05        12.43        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V 
       16.01        50.60        14.07        47.90        49.45        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM 
       53.10        43.76        18.02        26.20       117.40       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       18.05        25.28        13.28 

  AR MUTATED AR WILD-TYPE 
        6.02         0.07 
  AR MUTATED AR WILD-TYPE 
      106.55       194.79 
  AR MUTATED AR WILD-TYPE 
       31.20        37.02 
[1] "6.0 - 106.5 (31.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.4"
D12V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IV
  AR MUTATED         8        2         2        0
  AR WILD-TYPE     391       87       173       93
D12V3, multiclass
           clus
vv          AR MUTATED AR WILD-TYPE
  STAGE I            8          391
  STAGE II           2           87
  STAGE III          2          173
  STAGE IV           0           93
[1] 4 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
  AR MUTATED    10   2   2   0
  AR WILD-TYPE 413 109 235  11
D12V4, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  T1         10          413
  T2          2          109
  T3          2          235
  T4          0           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus            N0  N1  N2
  AR MUTATED     5   1   0
  AR WILD-TYPE 288  39   5
D12V5, multiclass
    clus
vv   AR MUTATED AR WILD-TYPE
  N0          5          288
  N1          1           39
  N2          0            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"
D12V6, binary
              cls
clus             0   1
  AR MUTATED     4   0
  AR WILD-TYPE 490  81
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      4    0
  AR WILD-TYPE  490   81
   clus
vv  AR MUTATED AR WILD-TYPE
  0          4          490
  1          0           81
[1] 2 2
[1] FALSE
D12V7, binary
              cls
clus             0   1
  AR MUTATED     6   9
  AR WILD-TYPE 252 517
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      6    9
  AR WILD-TYPE  252  517
        clus
vv       AR MUTATED AR WILD-TYPE
  FEMALE          6          252
  MALE            9          517
[1] 2 2
[1] FALSE
D12V8, continuous
              vv
clus           KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  AR MUTATED                    1                                 1
  AR WILD-TYPE                 65                               435
              vv
clus           KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AR MUTATED                                      13
  AR WILD-TYPE                                   269
D12V9, multiclass
                                       clus
vv                                      AR MUTATED AR WILD-TYPE
  KIDNEY CHROMOPHOBE                             1           65
  KIDNEY CLEAR CELL RENAL CARCINOMA              1          435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA         13          269
[1] 3 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 BLACK OR AFRICAN AMERICAN
  AR MUTATED                                  0     0                         1
  AR WILD-TYPE                                2    14                        82
              vv
clus           WHITE
  AR MUTATED      14
  AR WILD-TYPE   649
D12V12, multiclass
                                  clus
vv                                 AR MUTATED AR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            2
  ASIAN                                     0           14
  BLACK OR AFRICAN AMERICAN                 1           82
  WHITE                                    14          649
[1] 4 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
  AR MUTATED     0  14
  AR WILD-TYPE  36 541
[1] "tbl2"
              cls
clus           [,1] [,2]
  AR MUTATED      0   14
  AR WILD-TYPE   36  541
                        clus
vv                       AR MUTATED AR WILD-TYPE
  HISPANIC OR LATINO              0           36
  NOT HISPANIC OR LATINO         14          541
[1] 2 2
[1] FALSE

Clustering(13) Variable = STAG2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED    10   5
  STAG2 WILD-TYPE 568 197
  STAG2 MUTATED STAG2 WILD-TYPE 
             15             765 
  STAG2 MUTATED STAG2 WILD-TYPE 
              5             197 
$`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-4A-A93X TCGA-A4-7287 TCGA-A4-8098 TCGA-B3-4104 
       58.75        22.52        12.82        19.63        29.46        34.49 
TCGA-BQ-5875 TCGA-HE-7130 TCGA-IA-A83T 
       86.76        58.19        88.24 

$`STAG2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 
        1.41         4.57         2.53         3.48        19.00         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       123.09        79.89       131.15 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       35.21         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 
       49.18        49.28        50.33        54.48        38.56         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       47.08        69.21        14.66        63.39       107.41        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-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        30.58 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        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-IA-A83S TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
        2.04        85.78        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  STAG2 MUTATED STAG2 WILD-TYPE 
          12.82            0.07 
  STAG2 MUTATED STAG2 WILD-TYPE 
         130.65          194.79 
  STAG2 MUTATED STAG2 WILD-TYPE 
          45.14           36.95 
[1] "12.8 - 130.7 (45.1)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1.1"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         3        1         7        3
  STAG2 WILD-TYPE     396       88       168       90
D13V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               3             396
  STAGE II              1              88
  STAGE III             7             168
  STAGE IV              3              90
[1] 4 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     3   2   8   1
  STAG2 WILD-TYPE 420 109 229  10
D13V4, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  T1             3             420
  T2             2             109
  T3             8             229
  T4             1              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
  STAG2 MUTATED     4   1   0
  STAG2 WILD-TYPE 289  39   5
D13V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             4             289
  N1             1              39
  N2             0               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"
D13V6, binary
                 cls
clus                0   1
  STAG2 MUTATED     9   2
  STAG2 WILD-TYPE 485  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      9    2
  STAG2 WILD-TYPE  485   79
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0             9             485
  1             2              79
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  STAG2 MUTATED     7   8
  STAG2 WILD-TYPE 251 518
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      7    8
  STAG2 WILD-TYPE  251  518
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             7             251
  MALE               8             518
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:" "STAG2 MUTATED"         
clus
  STAG2 MUTATED STAG2 WILD-TYPE 
              2             124 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DW-7836      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-SX-A7SO      TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861 
"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-EU-5904      TCGA-EU-5905 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-EU-5906      TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-A4-7286 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0      TCGA-G7-6789 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR 
"STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" "STAG2 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL      TCGA-V9-A7HT 
"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                                       7
  STAG2 WILD-TYPE                                   275
D13V9, multiclass
                                       clus
vv                                      STAG2 MUTATED STAG2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 8             428
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             7             275
[1] 3 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
  STAG2 MUTATED                                  0     0
  STAG2 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED                           2    11
  STAG2 WILD-TYPE                        81   652
D13V12, multiclass
                                  clus
vv                                 STAG2 MUTATED STAG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    2              81
  WHITE                                       11             652
[1] 4 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
  STAG2 MUTATED     0  10
  STAG2 WILD-TYPE  36 545
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0   10
  STAG2 WILD-TYPE   36  545
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO            10             545
[1] 2 2
[1] FALSE

Clustering(14) Variable = KRAS MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  KRAS MUTATED     6   0
  KRAS WILD-TYPE 572 202
  KRAS MUTATED KRAS WILD-TYPE 
             6            774 
  KRAS MUTATED KRAS WILD-TYPE 
             0            202 
$`KRAS MUTATED`
TCGA-B0-5400 TCGA-2Z-A9JN TCGA-A4-8312 TCGA-BQ-5883 TCGA-GL-A9DC TCGA-MH-A854 
       56.98        24.33        23.28        40.83        12.89        17.62 

$`KRAS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 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-B0-5402 
       52.87        51.02        38.43        48.82        46.39        42.41 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A4-8515 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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       21.63        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       30.38        27.65        20.25        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  KRAS MUTATED KRAS WILD-TYPE 
         12.89           0.07 
  KRAS MUTATED KRAS WILD-TYPE 
         56.98         194.79 
  KRAS MUTATED KRAS WILD-TYPE 
        23.805         37.120 
[1] "12.9 - 57.0 (23.8)" "0.1 - 194.8 (37.1)"
[1] "hr="     "3300000"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KRAS MUTATED         5        0         1        0
  KRAS WILD-TYPE     394       89       174       93
D14V3, multiclass
           clus
vv          KRAS MUTATED KRAS WILD-TYPE
  STAGE I              5            394
  STAGE II             0             89
  STAGE III            1            174
  STAGE IV             0             93
[1] 4 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
  KRAS MUTATED     5   0   1   0
  KRAS WILD-TYPE 418 111 236  11
D14V4, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  T1            5            418
  T2            0            111
  T3            1            236
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  KRAS MUTATED     2   0   0
  KRAS WILD-TYPE 291  40   5
D14V5, multiclass
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            336 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8329 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KO-8405     TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A3-3357     TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A3-3373     TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3451 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5092     TCGA-B0-5094 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5699 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4330     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BP-5198     TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CJ-4890     TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789     TCGA-G7-6793 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2     TCGA-KV-A74V 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-AAVL 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP     TCGA-SX-A7SS 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX     TCGA-Y8-A897 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D14V6, binary
                cls
clus               0   1
  KRAS MUTATED     2   0
  KRAS WILD-TYPE 492  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      2    0
  KRAS WILD-TYPE  492   81
   clus
vv  KRAS MUTATED KRAS WILD-TYPE
  0            2            492
  1            0             81
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  KRAS MUTATED     5   1
  KRAS WILD-TYPE 253 525
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      5    1
  KRAS WILD-TYPE  253  525
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE            5            253
  MALE              1            525
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2            124 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7836     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4622 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-EU-5904     TCGA-EU-5905 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EU-5906     TCGA-EU-5907     TCGA-2Z-A9JE     TCGA-2Z-A9JK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A48D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL     TCGA-SX-A7SM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SN     TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KRAS MUTATED                    0                                 1
  KRAS WILD-TYPE                 66                               435
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KRAS MUTATED                                       5
  KRAS WILD-TYPE                                   277
D14V9, multiclass
                                       clus
vv                                      KRAS MUTATED KRAS WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            277
[1] 3 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:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             92 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B8-5550     TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A856 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
D14V11, continuous
[1] "Remove cluster labels:" "KRAS MUTATED"          
clus
  KRAS MUTATED KRAS WILD-TYPE 
             2             65 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-A4-A48D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894     TCGA-Y8-A896 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-Y8-A8RY 
"KRAS WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KRAS MUTATED                                  0     0
  KRAS WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  KRAS MUTATED                           4     2
  KRAS WILD-TYPE                        79   661
D14V12, multiclass
                                  clus
vv                                 KRAS MUTATED KRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   4             79
  WHITE                                       2            661
[1] 4 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
  KRAS MUTATED     0   5
  KRAS WILD-TYPE  36 550
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED      0    5
  KRAS WILD-TYPE   36  550
                        clus
vv                       KRAS MUTATED KRAS WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            5            550
[1] 2 2
[1] FALSE

Clustering(15) Variable = SLC6A14 MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  SLC6A14 MUTATED     2   2
  SLC6A14 WILD-TYPE 576 200
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                4               776 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2               200 
$`SLC6A14 MUTATED`
TCGA-KO-8416 TCGA-BP-4972 TCGA-BP-4985 TCGA-G7-6789 
       90.48        49.38        31.30         4.01 

$`SLC6A14 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8417 TCGA-A3-3311 
      103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        48.89        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
             4.01              0.07 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
            90.48            194.79 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
           40.340            36.985 
[1] "4.0 - 90.5 (40.3)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "1.9"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC6A14 MUTATED         0        0         3        1
  SLC6A14 WILD-TYPE     399       89       172       92
D15V3, multiclass
           clus
vv          SLC6A14 MUTATED SLC6A14 WILD-TYPE
  STAGE I                 0               399
  STAGE II                0                89
  STAGE III               3               172
  STAGE IV                1                92
[1] 4 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     0   0   4   0
  SLC6A14 WILD-TYPE 423 111 233  11
D15V4, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  T1               0               423
  T2               0               111
  T3               4               233
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC6A14 MUTATED     2   0   1
  SLC6A14 WILD-TYPE 291  40   4
D15V5, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  N0               2               291
  N1               0                40
  N2               1                 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"
D15V6, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   0
  SLC6A14 WILD-TYPE 491  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    0
  SLC6A14 WILD-TYPE  491   81
   clus
vv  SLC6A14 MUTATED SLC6A14 WILD-TYPE
  0               3               491
  1               0                81
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     2   2
  SLC6A14 WILD-TYPE 256 524
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      2    2
  SLC6A14 WILD-TYPE  256  524
        clus
vv       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  FEMALE               2               256
  MALE                 2               524
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "SLC6A14 MUTATED"       
clus
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                1               125 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-5P-A9JU        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4858        TCGA-CZ-4861 
"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-EU-5904        TCGA-EU-5905 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-EU-5906        TCGA-EU-5907        TCGA-2Z-A9JE        TCGA-2Z-A9JK 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X        TCGA-4A-A93Y 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UZ-A9PL 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-V9-A7HT 
"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                                       1
  SLC6A14 WILD-TYPE                                   281
D15V9, multiclass
                                       clus
vv                                      SLC6A14 MUTATED SLC6A14 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               281
[1] 3 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:" "SLC6A14 MUTATED"       
clus
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                1                93 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B9-A44B        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-GL-A59T        TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       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-B8-5158        TCGA-B8-5164        TCGA-B8-5550 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-5P-A9KE        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-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-GL-A9DD        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-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-Y8-A8RY 
"SLC6A14 WILD-TYPE" 
D15V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A14 MUTATED                                  0     0
  SLC6A14 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC6A14 MUTATED                           0     4
  SLC6A14 WILD-TYPE                        83   659
D15V12, multiclass
                                  clus
vv                                 SLC6A14 MUTATED SLC6A14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      0                83
  WHITE                                          4               659
[1] 4 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
  SLC6A14 MUTATED     0   2
  SLC6A14 WILD-TYPE  36 553
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      0    2
  SLC6A14 WILD-TYPE   36  553
                        clus
vv                       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO               2               553
[1] 2 2
[1] FALSE

Clustering(16) Variable = SMARCA4 MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  SMARCA4 MUTATED    14   6
  SMARCA4 WILD-TYPE 564 196
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
               20               760 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                6               196 
$`SMARCA4 MUTATED`
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-DW-7840 TCGA-KN-8426 TCGA-A3-3322 TCGA-B0-4817 
       76.64        49.25         3.75         3.55        48.59        33.50 
TCGA-B0-4823 TCGA-B0-4843 TCGA-B0-5098 TCGA-B0-5702 TCGA-B4-5377 TCGA-BP-4963 
       14.93        10.52        52.08        71.41        12.00        60.30 
TCGA-BP-4964 TCGA-A4-8310 TCGA-G7-6790 TCGA-G7-A8LB TCGA-MH-A55Z TCGA-SX-A71R 
       61.22        25.64        51.78        17.98        27.78        47.90 
TCGA-UZ-A9PK TCGA-UZ-A9Q0 
      117.40       110.73 

$`SMARCA4 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-B1-A47M TCGA-B1-A47O 
       61.05        21.37         0.89        12.99        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       24.46        13.78        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3323 
       90.48        92.55        39.16        24.16        49.02        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77         6.02        36.53        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-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        80.91        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       21.57         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4967 TCGA-BP-4968 
       47.97        71.41        63.62        58.68         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        29.46        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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       13.08         2.40         1.18         0.43         4.01        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-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       16.01        50.60        14.07        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        18.02        26.20       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
             3.55              0.07 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           117.40            194.79 
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
           48.245            36.950 
[1] "3.5 - 117.4 (48.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.2"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCA4 MUTATED        12        1         4        3
  SMARCA4 WILD-TYPE     387       88       171       90
D16V3, multiclass
           clus
vv          SMARCA4 MUTATED SMARCA4 WILD-TYPE
  STAGE I                12               387
  STAGE II                1                88
  STAGE III               4               171
  STAGE IV                3                90
[1] 4 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
  SMARCA4 MUTATED    12   2   6   0
  SMARCA4 WILD-TYPE 411 109 231  11
D16V4, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  T1              12               411
  T2               2               109
  T3               6               231
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SMARCA4 MUTATED     7   0   0
  SMARCA4 WILD-TYPE 286  40   5
D16V5, multiclass
    clus
vv   SMARCA4 MUTATED SMARCA4 WILD-TYPE
  N0               7               286
  N1               0                40
  N2               0                 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"
D16V6, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED    10   2
  SMARCA4 WILD-TYPE 484  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED     10    2
  SMARCA4 WILD-TYPE  484   79
   clus
vv  SMARCA4 MUTATED SMARCA4 WILD-TYPE
  0              10               484
  1               2                79
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  SMARCA4 MUTATED     4  16
  SMARCA4 WILD-TYPE 254 510
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      4   16
  SMARCA4 WILD-TYPE  254  510
        clus
vv       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  FEMALE               4               254
  MALE                16               510
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SMARCA4 MUTATED                    1                                 9
  SMARCA4 WILD-TYPE                 65                               427
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SMARCA4 MUTATED                                      10
  SMARCA4 WILD-TYPE                                   272
D16V9, multiclass
                                       clus
vv                                      SMARCA4 MUTATED SMARCA4 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   9               427
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              10               272
[1] 3 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:" "SMARCA4 MUTATED"       
clus
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                2                92 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-B9-A44B        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-GL-A59T        TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-AK-3451        TCGA-B8-4146        TCGA-B8-5158        TCGA-B8-5164 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-B8-5550        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-A48D        TCGA-A4-A57E 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854        TCGA-MH-A856 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
D16V11, continuous
[1] "Remove cluster labels:" "SMARCA4 MUTATED"       
clus
  SMARCA4 MUTATED SMARCA4 WILD-TYPE 
                1                66 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3451        TCGA-B8-5158        TCGA-B8-5550 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6793 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LD        TCGA-G7-A8LE 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6        TCGA-Q2-A5QZ 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RY 
"SMARCA4 WILD-TYPE" "SMARCA4 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCA4 MUTATED                                  0     0
  SMARCA4 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCA4 MUTATED                           3    17
  SMARCA4 WILD-TYPE                        80   646
D16V12, multiclass
                                  clus
vv                                 SMARCA4 MUTATED SMARCA4 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      3                80
  WHITE                                         17               646
[1] 4 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
  SMARCA4 MUTATED     0  17
  SMARCA4 WILD-TYPE  36 538
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCA4 MUTATED      0   17
  SMARCA4 WILD-TYPE   36  538
                        clus
vv                       SMARCA4 MUTATED SMARCA4 WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO              17               538
[1] 2 2
[1] FALSE

Clustering(17) Variable = NFE2L2 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     9   3
  NFE2L2 WILD-TYPE 569 199
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              12              768 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3              199 
$`NFE2L2 MUTATED`
TCGA-BP-5178 TCGA-B1-A47M TCGA-B0-4837 TCGA-B0-5097 TCGA-B2-4098 TCGA-BP-4768 
       62.86        21.67        45.30        21.86         1.68        13.15 
TCGA-CZ-5456 TCGA-4A-A93X TCGA-BQ-5881 TCGA-BQ-7044 TCGA-BQ-7051 TCGA-J7-A8I2 
       79.63        12.82        47.80       123.62        50.40        10.09 

$`NFE2L2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 
       41.62        27.62        35.90        48.10        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47O 
       21.37         0.89        12.99        76.64        49.25        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       32.61        35.90        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4770 
       77.98         5.98        41.75        71.80        48.07        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82        79.53        23.74        18.44        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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         7.92         2.76        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       61.28        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1.68             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          123.62           194.79 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          33.580           36.985 
[1] "1.7 - 123.6 (33.6)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.1"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         5        2         3        2
  NFE2L2 WILD-TYPE     394       87       172       91
D17V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                5              394
  STAGE II               2               87
  STAGE III              3              172
  STAGE IV               2               91
[1] 4 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     5   2   5   0
  NFE2L2 WILD-TYPE 418 109 232  11
D17V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              5              418
  T2              2              109
  T3              5              232
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NFE2L2 MUTATED     6   1   0
  NFE2L2 WILD-TYPE 287  39   5
D17V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              6              287
  N1              1               39
  N2              0                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"
D17V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     9   1
  NFE2L2 WILD-TYPE 485  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      9    1
  NFE2L2 WILD-TYPE  485   80
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              9              485
  1              1               80
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     3   9
  NFE2L2 WILD-TYPE 255 517
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      3    9
  NFE2L2 WILD-TYPE  255  517
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              3              255
  MALE                9              517
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"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-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-A4-7286       TCGA-A4-7828 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"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                                       6
  NFE2L2 WILD-TYPE                                   276
D17V9, multiclass
                                       clus
vv                                      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              6              276
[1] 3 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
  NFE2L2 MUTATED                                  0     1
  NFE2L2 WILD-TYPE                                2    13
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           2     9
  NFE2L2 WILD-TYPE                        81   654
D17V12, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         1               13
  BLACK OR AFRICAN AMERICAN                     2               81
  WHITE                                         9              654
[1] 4 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
  NFE2L2 MUTATED     0   7
  NFE2L2 WILD-TYPE  36 548
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0    7
  NFE2L2 WILD-TYPE   36  548
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              7              548
[1] 2 2
[1] FALSE

Clustering(18) Variable = ARID1A MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    13   5
  ARID1A WILD-TYPE 565 197
  ARID1A MUTATED ARID1A WILD-TYPE 
              18              762 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5              197 
$`ARID1A MUTATED`
TCGA-BP-5199 TCGA-PJ-A5Z8 TCGA-B0-5102 TCGA-B0-5692 TCGA-B0-5713 TCGA-B8-5549 
       44.55        19.73        90.87       129.67        91.46         6.38 
TCGA-CJ-4912 TCGA-CJ-6032 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-2Z-A9J5 
       54.48       119.64        18.77        47.08        14.66       100.27 
TCGA-A4-8515 TCGA-BQ-5878 TCGA-G7-6796 TCGA-HE-A5NJ TCGA-J7-8537 TCGA-UZ-A9Q0 
       23.31        63.72        71.44        56.75        10.55       110.73 

$`ARID1A WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       29.26        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5104 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-B0-5696 TCGA-B0-5697 
       48.82        46.39        56.98        42.41        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 
      123.09       130.65        79.89       131.15        89.49        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        53.42        62.66         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
        1.35        83.90        25.45        69.21        58.75        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 
        4.18         7.04        75.55        59.01        58.22        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       25.64        23.97        23.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       90.90        11.05        39.25        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       47.47        65.13        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.38             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          129.67           194.79 
  ARID1A MUTATED ARID1A WILD-TYPE 
          55.615           36.690 
[1] "6.4 - 129.7 (55.6)" "0.1 - 194.8 (36.7)"
[1] "hr=" "1.2"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         6        5         5        1
  ARID1A WILD-TYPE     393       84       170       92
D18V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                6              393
  STAGE II               5               84
  STAGE III              5              170
  STAGE IV               1               92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ARID1A MUTATED     7   5   6   0
  ARID1A WILD-TYPE 416 106 231  11
D18V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              7              416
  T2              5              106
  T3              6              231
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARID1A MUTATED     5   2   0
  ARID1A WILD-TYPE 288  38   5
D18V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              5              288
  N1              2               38
  N2              0                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"
D18V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    13   1
  ARID1A WILD-TYPE 481  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     13    1
  ARID1A WILD-TYPE  481   80
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             13              481
  1              1               80
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     7  11
  ARID1A WILD-TYPE 251 515
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      7   11
  ARID1A WILD-TYPE  251  515
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              7              251
  MALE               11              515
[1] 2 2
[1] FALSE
D18V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ARID1A MUTATED                    0                                10
  ARID1A WILD-TYPE                 66                               426
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ARID1A MUTATED                                       8
  ARID1A WILD-TYPE                                   274
D18V9, multiclass
                                       clus
vv                                      ARID1A MUTATED ARID1A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 10              426
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              8              274
[1] 3 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
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               92 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J7       TCGA-2Z-A9J8 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM       TCGA-2Z-A9JN 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NK       TCGA-IA-A40U 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854       TCGA-MH-A856 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ       TCGA-SX-A71S 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SR 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS       TCGA-UZ-A9PX 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896       TCGA-Y8-A8RY 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D18V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  1     1
  ARID1A WILD-TYPE                                1    13
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           0    15
  ARID1A WILD-TYPE                        83   648
D18V12, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         1               13
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                        15              648
[1] 4 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
  ARID1A MUTATED     2  12
  ARID1A WILD-TYPE  34 543
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2   12
  ARID1A WILD-TYPE   34  543
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2               34
  NOT HISPANIC OR LATINO             12              543
[1] 2 2
[1] FALSE

Clustering(19) Variable = BCLAF1 MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2                0   1
  BCLAF1 MUTATED     9   1
  BCLAF1 WILD-TYPE 569 201
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
              10              770 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1              201 
$`BCLAF1 MUTATED`
TCGA-KL-8328 TCGA-DZ-6134 TCGA-Y8-A895 TCGA-KL-8331 TCGA-CZ-5463 TCGA-EU-5905 
      102.81        61.02        15.91        98.96        21.76         3.91 
TCGA-A4-7286 TCGA-B9-7268 TCGA-BQ-5878 TCGA-BQ-5893 
       18.21        22.06        63.72         7.92 

$`BCLAF1 WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3358 
       28.11        23.28        28.80        47.24       130.13        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       86.37        21.60        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       23.84       109.22       137.06        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       14.63        22.78        62.63        18.12         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
            3.91             0.07 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
          102.81           194.79 
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
           21.91            37.12 
[1] "3.9 - 102.8 (21.9)" "0.1 - 194.8 (37.1)"
[1] "hr=" "2.4"
D19V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  BCLAF1 MUTATED         3        4         1        1
  BCLAF1 WILD-TYPE     396       85       174       92
D19V3, multiclass
           clus
vv          BCLAF1 MUTATED BCLAF1 WILD-TYPE
  STAGE I                3              396
  STAGE II               4               85
  STAGE III              1              174
  STAGE IV               1               92
[1] 4 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
  BCLAF1 MUTATED     3   4   3   0
  BCLAF1 WILD-TYPE 420 107 234  11
D19V4, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  T1              3              420
  T2              4              107
  T3              3              234
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  BCLAF1 MUTATED     3   2   0
  BCLAF1 WILD-TYPE 290  38   5
D19V5, multiclass
    clus
vv   BCLAF1 MUTATED BCLAF1 WILD-TYPE
  N0              3              290
  N1              2               38
  N2              0                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"
D19V6, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     6   1
  BCLAF1 WILD-TYPE 488  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      6    1
  BCLAF1 WILD-TYPE  488   80
   clus
vv  BCLAF1 MUTATED BCLAF1 WILD-TYPE
  0              6              488
  1              1               80
[1] 2 2
[1] FALSE
D19V7, binary
                  cls
clus                 0   1
  BCLAF1 MUTATED     3   7
  BCLAF1 WILD-TYPE 255 519
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      3    7
  BCLAF1 WILD-TYPE  255  519
        clus
vv       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  FEMALE              3              255
  MALE                7              519
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "BCLAF1 MUTATED"        
clus
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5906 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7828 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  BCLAF1 MUTATED                    2                                 2
  BCLAF1 WILD-TYPE                 64                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  BCLAF1 MUTATED                                       6
  BCLAF1 WILD-TYPE                                   276
D19V9, multiclass
                                       clus
vv                                      BCLAF1 MUTATED BCLAF1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              6              276
[1] 3 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:" "BCLAF1 MUTATED"        
clus
  BCLAF1 MUTATED BCLAF1 WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-5P-A9K3       TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-B9-4117       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" "BCLAF1 WILD-TYPE" 
      TCGA-Y8-A8RY 
"BCLAF1 WILD-TYPE" 
D19V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BCLAF1 MUTATED                                  0     0
  BCLAF1 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  BCLAF1 MUTATED                           0    10
  BCLAF1 WILD-TYPE                        83   653
D19V12, multiclass
                                  clus
vv                                 BCLAF1 MUTATED BCLAF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                        10              653
[1] 4 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
  BCLAF1 MUTATED     0   4
  BCLAF1 WILD-TYPE  36 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  BCLAF1 MUTATED      0    4
  BCLAF1 WILD-TYPE   36  551
                        clus
vv                       BCLAF1 MUTATED BCLAF1 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(20) Variable = ATM MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  ATM MUTATED    16   4
  ATM WILD-TYPE 562 198
  ATM MUTATED ATM WILD-TYPE 
           20           760 
  ATM MUTATED ATM WILD-TYPE 
            4           198 
$`ATM MUTATED`
TCGA-CJ-4904 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KN-8428 TCGA-KN-8435 TCGA-B0-5097 
      108.56        20.12       153.73        52.27       115.00        21.86 
TCGA-B0-5703 TCGA-B8-4622 TCGA-BP-4964 TCGA-BP-5173 TCGA-CJ-4639 TCGA-CJ-4900 
       73.84        50.14        61.22         2.04       106.16        56.35 
TCGA-CJ-5686 TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 TCGA-2Z-A9JK TCGA-A4-7997 
       67.00        14.66        63.42        12.26        38.99        30.48 
TCGA-WN-A9G9 TCGA-Y8-A8RY 
       26.01        25.28 

$`ATM WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       27.65       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       71.41       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       17.19        25.55        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       58.68        60.30         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       37.48        35.21        28.87         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        46.55        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 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
      109.84        50.24        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       62.10        73.35        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5453 
       69.21        58.75        63.39       107.41        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-EU-5904 TCGA-EU-5905 
       65.65        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       51.52        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
       35.18        19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         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-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
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-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        31.73        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05         6.02        13.28 

  ATM MUTATED ATM WILD-TYPE 
         2.04          0.07 
  ATM MUTATED ATM WILD-TYPE 
       153.73        194.79 
  ATM MUTATED ATM WILD-TYPE 
       51.205        36.900 
[1] "2.0 - 153.7 (51.2)" "0.1 - 194.8 (36.9)"
[1] "hr=" "1.5"
D20V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         8        6         3        3
  ATM WILD-TYPE     391       83       172       90
D20V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             8           391
  STAGE II            6            83
  STAGE III           3           172
  STAGE IV            3            90
[1] 4 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     8   6   5   1
  ATM WILD-TYPE 415 105 232  10
D20V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           8           415
  T2           6           105
  T3           5           232
  T4           1            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
  ATM MUTATED    10   1   0
  ATM WILD-TYPE 283  39   5
D20V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0          10           283
  N1           1            39
  N2           0             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"
D20V6, binary
               cls
clus              0   1
  ATM MUTATED    12   3
  ATM WILD-TYPE 482  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     12    3
  ATM WILD-TYPE  482   78
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          12           482
  1           3            78
[1] 2 2
[1] FALSE
D20V7, binary
               cls
clus              0   1
  ATM MUTATED     8  12
  ATM WILD-TYPE 250 514
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      8   12
  ATM WILD-TYPE  250  514
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           8           250
  MALE            12           514
[1] 2 2
[1] FALSE
D20V8, continuous
               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                                       5
  ATM WILD-TYPE                                   277
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           5           277
[1] 3 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
D20V11, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            2            65 
   TCGA-2Z-A9JD    TCGA-DW-5561    TCGA-PJ-A5Z9    TCGA-PJ-A8JU    TCGA-SX-A71W 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-UZ-A9PO    TCGA-UZ-A9PR    TCGA-Y8-A8RZ    TCGA-KL-8330    TCGA-KL-8335 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8433    TCGA-KO-8408 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KO-8409    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-5158    TCGA-B8-5550 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-2Z-A9J3    TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JN 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-2Z-A9JO    TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-A4-A48D    TCGA-A4-A57E 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-A5Y0    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-B9-4117    TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G    TCGA-G7-6793 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-7501    TCGA-G7-A8LB    TCGA-G7-A8LD    TCGA-G7-A8LE 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-A9DD    TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-MH-A854 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-MH-A856    TCGA-P4-A5E6    TCGA-Q2-A5QZ    TCGA-SX-A71S    TCGA-SX-A71U 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-UZ-A9PM 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-UZ-A9PS    TCGA-UZ-A9PX    TCGA-WN-AB4C    TCGA-Y8-A894    TCGA-Y8-A896 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     0
  ATM WILD-TYPE                                2    14
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           0    20
  ATM WILD-TYPE                        83   643
D20V12, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            14
  BLACK OR AFRICAN AMERICAN                  0            83
  WHITE                                     20           643
[1] 4 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  13
  ATM WILD-TYPE  35 542
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1   13
  ATM WILD-TYPE   35  542
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            35
  NOT HISPANIC OR LATINO          13           542
[1] 2 2
[1] FALSE

Clustering(21) Variable = CACNA1C MUTATION ANALYSIS
D21V1, survival
                   sevent
clus2                 0   1
  CACNA1C MUTATED     9   6
  CACNA1C WILD-TYPE 569 196
  CACNA1C MUTATED CACNA1C WILD-TYPE 
               15               765 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
                6               196 
$`CACNA1C MUTATED`
TCGA-KL-8339 TCGA-KL-8327 TCGA-KL-8346 TCGA-A3-3331 TCGA-AK-3460 TCGA-B0-4844 
       28.11       137.06        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-2Z-A9JK TCGA-BQ-5877 TCGA-DZ-6133 
       38.99         8.88        51.19 

$`CACNA1C WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3358 
      102.81        23.28        28.80        47.24       130.13        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73        23.84       109.22        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        54.74       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 
       94.29        83.21        37.58        38.40        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        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-B0-5092 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-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-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       23.74        18.44        79.63        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JM 
        4.57        91.73        56.81        54.64        51.52        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        86.76        19.27        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  CACNA1C MUTATED CACNA1C WILD-TYPE 
             8.88              0.07 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
           137.06            194.79 
  CACNA1C MUTATED CACNA1C WILD-TYPE 
            48.82             36.95 
[1] "8.9 - 137.1 (48.8)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.3"
D21V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CACNA1C MUTATED         4        1         4        6
  CACNA1C WILD-TYPE     395       88       171       87
D21V3, multiclass
           clus
vv          CACNA1C MUTATED CACNA1C WILD-TYPE
  STAGE I                 4               395
  STAGE II                1                88
  STAGE III               4               171
  STAGE IV                6                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
  CACNA1C MUTATED     5   2   8   0
  CACNA1C WILD-TYPE 418 109 229  11
D21V4, multiclass
    clus
vv   CACNA1C MUTATED CACNA1C WILD-TYPE
  T1               5               418
  T2               2               109
  T3               8               229
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CACNA1C MUTATED     4   4   0
  CACNA1C WILD-TYPE 289  36   5
D21V5, multiclass
    clus
vv   CACNA1C MUTATED CACNA1C WILD-TYPE
  N0               4               289
  N1               4                36
  N2               0                 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"
D21V6, binary
                   cls
clus                  0   1
  CACNA1C MUTATED     7   6
  CACNA1C WILD-TYPE 487  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      7    6
  CACNA1C WILD-TYPE  487   75
   clus
vv  CACNA1C MUTATED CACNA1C WILD-TYPE
  0               7               487
  1               6                75
[1] 2 2
[1] FALSE
D21V7, binary
                   cls
clus                  0   1
  CACNA1C MUTATED     5  10
  CACNA1C WILD-TYPE 253 516
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      5   10
  CACNA1C WILD-TYPE  253  516
        clus
vv       CACNA1C MUTATED CACNA1C WILD-TYPE
  FEMALE               5               253
  MALE                10               516
[1] 2 2
[1] FALSE
D21V8, continuous
[1] "Remove cluster labels:" "CACNA1C MUTATED"       
clus
  CACNA1C MUTATED CACNA1C WILD-TYPE 
                2               124 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-5P-A9JU        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4858        TCGA-CZ-4861 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-CZ-5982        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-EU-5907        TCGA-2Z-A9JE        TCGA-2Z-A9JN        TCGA-4A-A93W 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-A4-A6HP        TCGA-AL-3466        TCGA-DW-7963        TCGA-EV-5901 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A7Q0        TCGA-G7-6789 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
                   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                                       3
  CACNA1C WILD-TYPE                                   279
D21V9, multiclass
                                       clus
vv                                      CACNA1C MUTATED CACNA1C WILD-TYPE
  KIDNEY CHROMOPHOBE                                  3                63
  KIDNEY CLEAR CELL RENAL CARCINOMA                   9               427
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               279
[1] 3 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
[1] "Remove cluster labels:" "CACNA1C MUTATED"       
clus
  CACNA1C MUTATED CACNA1C WILD-TYPE 
                1                93 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B9-A44B        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-GL-A59T        TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       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-B8-5158        TCGA-B8-5164 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-B8-5550        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JM        TCGA-2Z-A9JN 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-5P-A9KE        TCGA-A4-8310        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-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-GL-A9DD        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-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" "CACNA1C WILD-TYPE" 
       TCGA-Y8-A8RY 
"CACNA1C WILD-TYPE" 
D21V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CACNA1C MUTATED                                  0     0
  CACNA1C WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CACNA1C MUTATED                           1    14
  CACNA1C WILD-TYPE                        82   649
D21V12, multiclass
                                  clus
vv                                 CACNA1C MUTATED CACNA1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      1                82
  WHITE                                         14               649
[1] 4 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
  CACNA1C MUTATED     1   9
  CACNA1C WILD-TYPE  35 546
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CACNA1C MUTATED      1    9
  CACNA1C WILD-TYPE   35  546
                        clus
vv                       CACNA1C MUTATED CACNA1C WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO               9               546
[1] 2 2
[1] FALSE

Clustering(22) Variable = PARD6B MUTATION ANALYSIS
D22V1, survival
                  sevent
clus2                0   1
  PARD6B MUTATED     7   1
  PARD6B WILD-TYPE 571 201
  PARD6B MUTATED PARD6B WILD-TYPE 
               8              772 
  PARD6B MUTATED PARD6B WILD-TYPE 
               1              201 
$`PARD6B MUTATED`
TCGA-B0-5694 TCGA-A4-7584 TCGA-BQ-5886 TCGA-B0-5702 TCGA-2Z-A9JG TCGA-B9-A8YI 
       15.78        21.37        26.04        71.41        54.64        12.30 
TCGA-BQ-7044 TCGA-GL-A9DE 
      123.62        16.31 

$`PARD6B WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 
       43.96        52.21        18.51       112.80       133.94        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5888 
       21.07        10.16        21.86        11.87        19.23        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        80.91        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        56.81        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2.76        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.43        12.89        11.21        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  PARD6B MUTATED PARD6B WILD-TYPE 
           12.30             0.07 
  PARD6B MUTATED PARD6B WILD-TYPE 
          123.62           194.79 
  PARD6B MUTATED PARD6B WILD-TYPE 
          23.705           37.120 
[1] "12.3 - 123.6 (23.7)" "0.1 - 194.8 (37.1)" 
[1] "hr=" "2"  
D22V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PARD6B MUTATED         5        0         3        0
  PARD6B WILD-TYPE     394       89       172       93
D22V3, multiclass
           clus
vv          PARD6B MUTATED PARD6B WILD-TYPE
  STAGE I                5              394
  STAGE II               0               89
  STAGE III              3              172
  STAGE IV               0               93
[1] 4 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     5   0   3   0
  PARD6B WILD-TYPE 418 111 234  11
D22V4, multiclass
    clus
vv   PARD6B MUTATED PARD6B WILD-TYPE
  T1              5              418
  T2              0              111
  T3              3              234
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PARD6B MUTATED     2   0   0
  PARD6B WILD-TYPE 291  40   5
D22V5, multiclass
[1] "Remove cluster labels:" "PARD6B MUTATED"        
clus
  PARD6B MUTATED PARD6B WILD-TYPE 
               2              336 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621       TCGA-BP-4158 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342       TCGA-BP-4795 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4995 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199       TCGA-BP-5201 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894       TCGA-CJ-4904 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-5P-A9JU 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657       TCGA-BQ-5888 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W       TCGA-Y8-A8RZ 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329       TCGA-KL-8330 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333       TCGA-KL-8334 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337       TCGA-KL-8338 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342       TCGA-KL-8343 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346       TCGA-KM-8438 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419       TCGA-KN-8421 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424       TCGA-KN-8425 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429       TCGA-KO-8405 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313       TCGA-A3-3317 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357 
"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-3427       TCGA-AK-3428       TCGA-AK-3429       TCGA-AK-3430 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3451       TCGA-AK-3456 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5699 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159       TCGA-B8-5163 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545       TCGA-B8-5546 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551       TCGA-B8-5553 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4159       TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4343 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351       TCGA-BP-4352 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761       TCGA-BP-4768 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787       TCGA-BP-4797 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4798       TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-4985       TCGA-BP-4989       TCGA-BP-5007       TCGA-BP-5010 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5198 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4638       TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4873       TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4900       TCGA-CJ-4918       TCGA-CJ-5678 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CJ-6033       TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-2Z-A9J1 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891       TCGA-BQ-5893 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048       TCGA-BQ-7050 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131       TCGA-F9-A8NY 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-F9-A97G       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-G7-A8LD       TCGA-GL-6846       TCGA-GL-7966 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U       TCGA-IA-A40Y 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2       TCGA-KV-A74V 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA       TCGA-P4-AAVL 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP       TCGA-SX-A7SS 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
      TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX       TCGA-Y8-A897 
"PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" "PARD6B WILD-TYPE" 
D22V6, binary
                  cls
clus                 0   1
  PARD6B MUTATED     4   0
  PARD6B WILD-TYPE 490  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      4    0
  PARD6B WILD-TYPE  490   81
   clus
vv  PARD6B MUTATED PARD6B WILD-TYPE
  0              4              490
  1              0               81
[1] 2 2
[1] FALSE
D22V7, binary
                  cls
clus                 0   1
  PARD6B MUTATED     0   8
  PARD6B WILD-TYPE 258 518
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      0    8
  PARD6B WILD-TYPE  258  518
        clus
vv       PARD6B MUTATED PARD6B WILD-TYPE
  FEMALE              0              258
  MALE                8              518
[1] 2 2
[1] FALSE
D22V8, 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                                       6
  PARD6B WILD-TYPE                                   276
D22V9, multiclass
                                       clus
vv                                      PARD6B MUTATED PARD6B WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              6              276
[1] 3 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
  PARD6B MUTATED                                  0     0
  PARD6B WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PARD6B MUTATED                           3     5
  PARD6B WILD-TYPE                        80   658
D22V12, multiclass
                                  clus
vv                                 PARD6B MUTATED PARD6B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     3               80
  WHITE                                         5              658
[1] 4 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
  PARD6B MUTATED     0   6
  PARD6B WILD-TYPE  36 549
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PARD6B MUTATED      0    6
  PARD6B WILD-TYPE   36  549
                        clus
vv                       PARD6B MUTATED PARD6B WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              6              549
[1] 2 2
[1] FALSE

Clustering(23) Variable = CUL3 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  CUL3 MUTATED    15   1
  CUL3 WILD-TYPE 563 201
  CUL3 MUTATED CUL3 WILD-TYPE 
            16            764 
  CUL3 MUTATED CUL3 WILD-TYPE 
             1            201 
$`CUL3 MUTATED`
TCGA-BP-4965 TCGA-DV-5574 TCGA-2Z-A9JQ TCGA-Y8-A8RZ TCGA-BP-4963 TCGA-BP-5175 
       61.51        66.28        25.58         6.74        60.30        30.64 
TCGA-CJ-4876 TCGA-CZ-5457 TCGA-2Z-A9J8 TCGA-5P-A9KA TCGA-A4-A57E TCGA-A4-A5Y0 
       64.27        90.54        91.73        12.99         8.48         8.28 
TCGA-AL-7173 TCGA-B9-A8YI TCGA-BQ-5885 TCGA-P4-A5E6 
       67.73        12.30        30.28        99.78 

$`CUL3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS 
       56.84        23.90        34.85        39.88        33.07        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       21.60        15.91        15.62        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
        6.71        47.97        71.41        63.62        58.68        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87         6.35        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06       116.84        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       43.04        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       15.75        12.46         9.63        70.19        66.71        62.66 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
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-5887 TCGA-BQ-5889 
       47.80        21.63        40.83        26.04        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       31.13        15.48        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  CUL3 MUTATED CUL3 WILD-TYPE 
          6.74           0.07 
  CUL3 MUTATED CUL3 WILD-TYPE 
         99.78         194.79 
  CUL3 MUTATED CUL3 WILD-TYPE 
        45.470         36.985 
[1] "6.7 - 99.8 (45.5)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "4.5"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  CUL3 MUTATED         9        1         3        2
  CUL3 WILD-TYPE     390       88       172       91
D23V3, multiclass
           clus
vv          CUL3 MUTATED CUL3 WILD-TYPE
  STAGE I              9            390
  STAGE II             1             88
  STAGE III            3            172
  STAGE IV             2             91
[1] 4 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
  CUL3 MUTATED    11   2   3   0
  CUL3 WILD-TYPE 412 109 234  11
D23V4, multiclass
    clus
vv   CUL3 MUTATED CUL3 WILD-TYPE
  T1           11            412
  T2            2            109
  T3            3            234
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  CUL3 MUTATED     4   1   1
  CUL3 WILD-TYPE 289  39   4
D23V5, multiclass
    clus
vv   CUL3 MUTATED CUL3 WILD-TYPE
  N0            4            289
  N1            1             39
  N2            1              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"
D23V6, binary
                cls
clus               0   1
  CUL3 MUTATED     8   1
  CUL3 WILD-TYPE 486  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      8    1
  CUL3 WILD-TYPE  486   80
   clus
vv  CUL3 MUTATED CUL3 WILD-TYPE
  0            8            486
  1            1             80
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  CUL3 MUTATED     2  14
  CUL3 WILD-TYPE 256 512
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      2   14
  CUL3 WILD-TYPE  256  512
        clus
vv       CUL3 MUTATED CUL3 WILD-TYPE
  FEMALE            2            256
  MALE             14            512
[1] 2 2
[1] FALSE
D23V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CUL3 MUTATED                    0                                 6
  CUL3 WILD-TYPE                 66                               430
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CUL3 MUTATED                                      10
  CUL3 WILD-TYPE                                   272
D23V9, multiclass
                                       clus
vv                                      CUL3 MUTATED CUL3 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                6            430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           10            272
[1] 3 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
D23V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CUL3 MUTATED                                  0     0
  CUL3 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  CUL3 MUTATED                           2    14
  CUL3 WILD-TYPE                        81   649
D23V12, multiclass
                                  clus
vv                                 CUL3 MUTATED CUL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   2             81
  WHITE                                      14            649
[1] 4 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
  CUL3 MUTATED     1  13
  CUL3 WILD-TYPE  35 542
[1] "tbl2"
                cls
clus             [,1] [,2]
  CUL3 MUTATED      1   13
  CUL3 WILD-TYPE   35  542
                        clus
vv                       CUL3 MUTATED CUL3 WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           13            542
[1] 2 2
[1] FALSE

Clustering(24) Variable = PIK3CA MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    10   5
  PIK3CA WILD-TYPE 568 197
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              15              765 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5              197 
$`PIK3CA MUTATED`
TCGA-BP-4160 TCGA-DZ-6134 TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-5713 TCGA-B8-5159 
       94.72        61.02        88.37         2.53        91.46        23.74 
TCGA-BP-4352 TCGA-BP-4960 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 TCGA-5P-A9K3 
       11.31        71.41        74.27        64.18         7.36        15.48 
TCGA-B9-A8YI TCGA-BQ-5893 TCGA-UZ-A9PL 
       12.30         7.92       103.63 

$`PIK3CA WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
      111.02        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       45.53        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       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-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 
      123.09       130.65        79.89       131.15        89.49        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 
       36.39        10.98        36.95         6.71        47.97        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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-4874 TCGA-CJ-4875 
       83.97        49.25        79.66        47.18        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-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       62.66       119.64        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
       25.35        10.82         7.66         0.95         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       117.40       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          103.63           194.79 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           61.02            36.95 
[1] "2.5 - 103.6 (61.0)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.2"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         4        3         4        3
  PIK3CA WILD-TYPE     395       86       171       90
D24V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                4              395
  STAGE II               3               86
  STAGE III              4              171
  STAGE IV               3               90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  PIK3CA MUTATED     4   4   7   0
  PIK3CA WILD-TYPE 419 107 230  11
D24V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              4              419
  T2              4              107
  T3              7              230
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3CA MUTATED     9   1   0
  PIK3CA WILD-TYPE 284  39   5
D24V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0              9              284
  N1              1               39
  N2              0                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"
D24V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   3
  PIK3CA WILD-TYPE 486  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    3
  PIK3CA WILD-TYPE  486   78
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              8              486
  1              3               78
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7   8
  PIK3CA WILD-TYPE 251 518
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    8
  PIK3CA WILD-TYPE  251  518
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              7              251
  MALE                8              518
[1] 2 2
[1] FALSE
D24V8, continuous
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-EU-5906       TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A71R       TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A7SQ       TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-V9-A7HT 
"PIK3CA WILD-TYPE" 
                  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                                       5
  PIK3CA WILD-TYPE                                   277
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              5              277
[1] 3 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
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-Y8-A8RY 
"PIK3CA WILD-TYPE" 
D24V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           1    14
  PIK3CA WILD-TYPE                        82   649
D24V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     1               82
  WHITE                                        14              649
[1] 4 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  12
  PIK3CA WILD-TYPE  35 543
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   12
  PIK3CA WILD-TYPE   35  543
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               35
  NOT HISPANIC OR LATINO             12              543
[1] 2 2
[1] FALSE

Clustering(25) Variable = SMARCB1 MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  SMARCB1 MUTATED     6   3
  SMARCB1 WILD-TYPE 572 199
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                9               771 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                3               199 
$`SMARCB1 MUTATED`
TCGA-AK-3455 TCGA-CJ-6030 TCGA-5P-A9JU TCGA-B1-A47M TCGA-KN-8428 TCGA-5P-A9KC 
       22.45        75.58        12.26        21.67        52.27        12.39 
TCGA-BQ-5876 TCGA-BQ-7048 TCGA-GL-6846 
       19.27        93.34       194.79 

$`SMARCB1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4712 
       42.97       109.91        58.49        28.73        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56       118.85       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       16.18        22.49        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        49.25        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8429 TCGA-KN-8431 
       65.19       104.52         3.55         0.99        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-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            12.26              0.07 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
           194.79            153.73 
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
            22.45             37.02 
[1] "12.3 - 194.8 (22.4)" "0.1 - 153.7 (37.0)" 
[1] "hr=" "1.2"
D25V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SMARCB1 MUTATED         2        1         4        1
  SMARCB1 WILD-TYPE     397       88       171       92
D25V3, multiclass
           clus
vv          SMARCB1 MUTATED SMARCB1 WILD-TYPE
  STAGE I                 2               397
  STAGE II                1                88
  STAGE III               4               171
  STAGE IV                1                92
[1] 4 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
  SMARCB1 MUTATED     3   1   4   1
  SMARCB1 WILD-TYPE 420 110 233  10
D25V4, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  T1               3               420
  T2               1               110
  T3               4               233
  T4               1                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
  SMARCB1 MUTATED     4   1   0
  SMARCB1 WILD-TYPE 289  39   5
D25V5, multiclass
    clus
vv   SMARCB1 MUTATED SMARCB1 WILD-TYPE
  N0               4               289
  N1               1                39
  N2               0                 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"
D25V6, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     5   0
  SMARCB1 WILD-TYPE 489  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      5    0
  SMARCB1 WILD-TYPE  489   81
   clus
vv  SMARCB1 MUTATED SMARCB1 WILD-TYPE
  0               5               489
  1               0                81
[1] 2 2
[1] FALSE
D25V7, binary
                   cls
clus                  0   1
  SMARCB1 MUTATED     2   7
  SMARCB1 WILD-TYPE 256 519
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      2    7
  SMARCB1 WILD-TYPE  256  519
        clus
vv       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  FEMALE               2               256
  MALE                 7               519
[1] 2 2
[1] FALSE
D25V8, continuous
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                1               125 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W        TCGA-SX-A7SO 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440        TCGA-KM-8443 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8429 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428        TCGA-AK-3430 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-5456 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-CZ-5982        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-EU-5907        TCGA-2Z-A9JE        TCGA-2Z-A9JK        TCGA-2Z-A9JN 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466        TCGA-DW-7963 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A7Q0 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UZ-A9PL 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-V9-A7HT 
"SMARCB1 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SMARCB1 MUTATED                    1                                 2
  SMARCB1 WILD-TYPE                 65                               434
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SMARCB1 MUTATED                                       6
  SMARCB1 WILD-TYPE                                   276
D25V9, multiclass
                                       clus
vv                                      SMARCB1 MUTATED SMARCB1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               6               276
[1] 3 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
[1] "Remove cluster labels:" "SMARCB1 MUTATED"       
clus
  SMARCB1 MUTATED SMARCB1 WILD-TYPE 
                2                92 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-B9-A44B 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU        TCGA-SX-A71W 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-KL-8324 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-KO-8416        TCGA-AK-3445        TCGA-AK-3451        TCGA-B8-4146 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-2Z-A9J2 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3        TCGA-5P-A9KE 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6792 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854        TCGA-MH-A856 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" "SMARCB1 WILD-TYPE" 
D25V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SMARCB1 MUTATED                                  0     0
  SMARCB1 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SMARCB1 MUTATED                           1     8
  SMARCB1 WILD-TYPE                        82   655
D25V12, multiclass
                                  clus
vv                                 SMARCB1 MUTATED SMARCB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      1                82
  WHITE                                          8               655
[1] 4 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
  SMARCB1 MUTATED     0   8
  SMARCB1 WILD-TYPE  36 547
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SMARCB1 MUTATED      0    8
  SMARCB1 WILD-TYPE   36  547
                        clus
vv                       SMARCB1 MUTATED SMARCB1 WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO               8               547
[1] 2 2
[1] FALSE

Clustering(26) Variable = PCF11 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  PCF11 MUTATED    10   3
  PCF11 WILD-TYPE 568 199
  PCF11 MUTATED PCF11 WILD-TYPE 
             13             767 
  PCF11 MUTATED PCF11 WILD-TYPE 
              3             199 
$`PCF11 MUTATED`
TCGA-BQ-7058 TCGA-DZ-6134 TCGA-PJ-A8JU TCGA-B0-5100 TCGA-BP-5184 TCGA-5P-A9JZ 
       11.28        61.02        12.49        62.89        37.25        90.21 
TCGA-B1-5398 TCGA-B9-4617 TCGA-BQ-5876 TCGA-BQ-7050 TCGA-EV-5903 TCGA-IA-A83S 
       41.13         1.15        19.27        61.28        24.89        85.78 
TCGA-SX-A71U 
       44.61 

$`PCF11 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12        48.85        13.61       129.86        35.93 
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-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       19.73        17.75        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9K0 
        0.13        12.82        11.57       106.55        49.58        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        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-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       93.34        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99         2.04        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL 
       50.60        14.07        47.90        49.45        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  PCF11 MUTATED PCF11 WILD-TYPE 
           1.15            0.07 
  PCF11 MUTATED PCF11 WILD-TYPE 
          90.21          194.79 
  PCF11 MUTATED PCF11 WILD-TYPE 
          41.13           36.95 
[1] "1.1 - 90.2 (41.1)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PCF11 MUTATED         7        0         3        0
  PCF11 WILD-TYPE     392       89       172       93
D26V3, multiclass
           clus
vv          PCF11 MUTATED PCF11 WILD-TYPE
  STAGE I               7             392
  STAGE II              0              89
  STAGE III             3             172
  STAGE IV              0              93
[1] 4 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
  PCF11 MUTATED     9   0   3   0
  PCF11 WILD-TYPE 414 111 234  11
D26V4, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  T1             9             414
  T2             0             111
  T3             3             234
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PCF11 MUTATED     2   0   0
  PCF11 WILD-TYPE 291  40   5
D26V5, multiclass
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2             336 
     TCGA-KL-8328      TCGA-KL-8339      TCGA-KN-8430      TCGA-A3-3358 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3450      TCGA-B0-5088      TCGA-B0-5691 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5698      TCGA-B8-4621 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4160      TCGA-BP-4331      TCGA-BP-4342 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4799      TCGA-BP-4986      TCGA-BP-4988 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5191      TCGA-BP-5199 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4891      TCGA-CJ-4894 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-6030      TCGA-CZ-4854      TCGA-CZ-4856 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8329 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418      TCGA-KN-8419 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423      TCGA-KN-8424 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8410      TCGA-KO-8413      TCGA-KO-8414 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KO-8415      TCGA-KO-8416      TCGA-KO-8417      TCGA-A3-3313 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347      TCGA-A3-3349 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A3-3357      TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A3-3373      TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3451 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691      TCGA-B0-4693 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810      TCGA-B0-4811 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817      TCGA-B0-4823 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5092      TCGA-B0-5094 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5400      TCGA-B0-5692      TCGA-B0-5696      TCGA-B0-5697 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B0-5712      TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4622      TCGA-B8-5158 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-5159      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-5551      TCGA-B8-5553      TCGA-BP-4159      TCGA-BP-4162 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4337      TCGA-BP-4338 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4340      TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4351      TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4761      TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4960 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4989 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BP-5186      TCGA-BP-5198      TCGA-CJ-4638      TCGA-CJ-4639 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4892      TCGA-CJ-4900 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6033      TCGA-CW-5585 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4857      TCGA-CZ-4859 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-4863      TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-5984      TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-A655 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131      TCGA-F9-A8NY 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846      TCGA-GL-7966 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U      TCGA-IA-A40Y 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2      TCGA-KV-A74V 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA      TCGA-P4-AAVL 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP      TCGA-SX-A7SS 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX      TCGA-Y8-A897 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
D26V6, binary
                 cls
clus                0   1
  PCF11 MUTATED     9   0
  PCF11 WILD-TYPE 485  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      9    0
  PCF11 WILD-TYPE  485   81
   clus
vv  PCF11 MUTATED PCF11 WILD-TYPE
  0             9             485
  1             0              81
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  PCF11 MUTATED     3  10
  PCF11 WILD-TYPE 255 516
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      3   10
  PCF11 WILD-TYPE  255  516
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  FEMALE             3             255
  MALE              10             516
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2             124 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7836      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SO      TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EU-5906      TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-F9-A7Q0 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL      TCGA-V9-A7HT 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PCF11 MUTATED                    0                                 2
  PCF11 WILD-TYPE                 66                               434
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PCF11 MUTATED                                      11
  PCF11 WILD-TYPE                                   271
D26V9, multiclass
                                       clus
vv                                      PCF11 MUTATED PCF11 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 2             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            11             271
[1] 3 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
D26V11, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              2              65 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-SX-A71W 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ      TCGA-KL-8330 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345      TCGA-KM-8639 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409      TCGA-AK-3445 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550      TCGA-2Z-A9J3 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-A4-A48D 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SR 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS      TCGA-UZ-A9PX 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894      TCGA-Y8-A896 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-Y8-A8RY 
"PCF11 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCF11 MUTATED                                  0     0
  PCF11 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PCF11 MUTATED                           2    11
  PCF11 WILD-TYPE                        81   652
D26V12, multiclass
                                  clus
vv                                 PCF11 MUTATED PCF11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    2              81
  WHITE                                       11             652
[1] 4 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
  PCF11 MUTATED     1   9
  PCF11 WILD-TYPE  35 546
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      1    9
  PCF11 WILD-TYPE   35  546
                        clus
vv                       PCF11 MUTATED PCF11 WILD-TYPE
  HISPANIC OR LATINO                 1              35
  NOT HISPANIC OR LATINO             9             546
[1] 2 2
[1] FALSE

Clustering(27) Variable = WASL MUTATION ANALYSIS
D27V1, survival
                sevent
clus2              0   1
  WASL MUTATED     5   3
  WASL WILD-TYPE 573 199
  WASL MUTATED WASL WILD-TYPE 
             8            772 
  WASL MUTATED WASL WILD-TYPE 
             3            199 
$`WASL MUTATED`
TCGA-BP-5006 TCGA-KN-8428 TCGA-B0-4852 TCGA-B0-5697 TCGA-B0-5709 TCGA-BP-4985 
       27.62        52.27        36.85        86.47       130.65        31.30 
TCGA-UZ-A9PP TCGA-UZ-A9PV 
       98.96        47.47 

$`WASL WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       41.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.99        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
        2.27        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5699 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-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      123.09        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         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-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
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-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 
      125.29        37.35        71.24        30.67        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  WASL MUTATED WASL WILD-TYPE 
         27.62           0.07 
  WASL MUTATED WASL WILD-TYPE 
        130.65         194.79 
  WASL MUTATED WASL WILD-TYPE 
         49.87          36.95 
[1] "27.6 - 130.7 (49.9)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1"  
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  WASL MUTATED         4        2         2        0
  WASL WILD-TYPE     395       87       173       93
D27V3, multiclass
           clus
vv          WASL MUTATED WASL WILD-TYPE
  STAGE I              4            395
  STAGE II             2             87
  STAGE III            2            173
  STAGE IV             0             93
[1] 4 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
  WASL MUTATED     4   2   2   0
  WASL WILD-TYPE 419 109 235  11
D27V4, multiclass
    clus
vv   WASL MUTATED WASL WILD-TYPE
  T1            4            419
  T2            2            109
  T3            2            235
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  WASL MUTATED     5   0   0
  WASL WILD-TYPE 288  40   5
D27V5, multiclass
    clus
vv   WASL MUTATED WASL WILD-TYPE
  N0            5            288
  N1            0             40
  N2            0              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"
D27V6, binary
                cls
clus               0   1
  WASL MUTATED     5   0
  WASL WILD-TYPE 489  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  WASL MUTATED      5    0
  WASL WILD-TYPE  489   81
   clus
vv  WASL MUTATED WASL WILD-TYPE
  0            5            489
  1            0             81
[1] 2 2
[1] FALSE
D27V7, binary
                cls
clus               0   1
  WASL MUTATED     2   6
  WASL WILD-TYPE 256 520
[1] "tbl2"
                cls
clus             [,1] [,2]
  WASL MUTATED      2    6
  WASL WILD-TYPE  256  520
        clus
vv       WASL MUTATED WASL WILD-TYPE
  FEMALE            2            256
  MALE              6            520
[1] 2 2
[1] FALSE
D27V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  WASL MUTATED                    1                                 5
  WASL WILD-TYPE                 65                               431
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  WASL MUTATED                                       2
  WASL WILD-TYPE                                   280
D27V9, multiclass
                                       clus
vv                                      WASL MUTATED WASL WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                5            431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            280
[1] 3 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
[1] "Remove cluster labels:" "WASL MUTATED"          
clus
  WASL MUTATED WASL WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445     TCGA-AK-3451 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164     TCGA-B8-5550 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896 
"WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" "WASL WILD-TYPE" 
    TCGA-Y8-A8RY 
"WASL WILD-TYPE" 
D27V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  WASL MUTATED                                  0     0
  WASL WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  WASL MUTATED                           0     8
  WASL WILD-TYPE                        83   655
D27V12, multiclass
                                  clus
vv                                 WASL MUTATED WASL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                       8            655
[1] 4 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
  WASL MUTATED     0   6
  WASL WILD-TYPE  36 549
[1] "tbl2"
                cls
clus             [,1] [,2]
  WASL MUTATED      0    6
  WASL WILD-TYPE   36  549
                        clus
vv                       WASL MUTATED WASL WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            6            549
[1] 2 2
[1] FALSE

Clustering(28) Variable = DNMT3A MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    10   1
  DNMT3A WILD-TYPE 568 201
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              11              769 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               1              201 
$`DNMT3A MUTATED`
TCGA-BP-4160 TCGA-BP-4999 TCGA-BP-5181 TCGA-GL-A59T TCGA-B0-5120 TCGA-B0-5697 
       94.72        41.62        49.15        17.95        38.43        86.47 
TCGA-B4-5836 TCGA-2Z-A9J1 TCGA-IA-A40Y TCGA-MH-A55Z TCGA-UZ-A9PJ 
        4.64        75.55         2.04        27.78        26.20 

$`DNMT3A WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
      111.02        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5006 
       53.65        25.81        27.22         5.82        45.07        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       35.90        48.10        62.86        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 
       31.27        63.25        26.93        27.65       108.56       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       23.90        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-HE-A5NF 
       13.78         3.75        14.63         3.02        61.02        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        52.87        51.02        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5701 
       56.98        42.41       129.67        85.78       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        5.10         1.25         0.53         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       34.29        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        18.02       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            2.04             0.07 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           94.72           194.79 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           38.43            36.95 
[1] "2.0 - 94.7 (38.4)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "2.8"
D28V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  DNMT3A MUTATED         9        0         2        0
  DNMT3A WILD-TYPE     390       89       173       93
D28V3, multiclass
           clus
vv          DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                9              390
  STAGE II               0               89
  STAGE III              2              173
  STAGE IV               0               93
[1] 4 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
  DNMT3A MUTATED     9   0   2   0
  DNMT3A WILD-TYPE 414 111 235  11
D28V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              9              414
  T2              0              111
  T3              2              235
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNMT3A MUTATED     5   1   0
  DNMT3A WILD-TYPE 288  39   5
D28V5, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  N0              5              288
  N1              1               39
  N2              0                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"
D28V6, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     6   0
  DNMT3A WILD-TYPE 488  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      6    0
  DNMT3A WILD-TYPE  488   81
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0              6              488
  1              0               81
[1] 2 2
[1] FALSE
D28V7, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     4   7
  DNMT3A WILD-TYPE 254 519
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      4    7
  DNMT3A WILD-TYPE  254  519
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              4              254
  MALE                7              519
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5838       TCGA-B4-5843 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-5456 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  DNMT3A MUTATED                    0                                 6
  DNMT3A WILD-TYPE                 66                               430
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DNMT3A MUTATED                                       5
  DNMT3A WILD-TYPE                                   277
D28V9, multiclass
                                       clus
vv                                      DNMT3A MUTATED DNMT3A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              5              277
[1] 3 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
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU       TCGA-SX-A71W 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ       TCGA-KL-8324 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433       TCGA-KO-8408 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445       TCGA-AK-3451 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164       TCGA-B8-5550 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7       TCGA-2Z-A9J8 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM       TCGA-2Z-A9JN 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-Y8-A8RY 
"DNMT3A WILD-TYPE" 
D28V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT3A MUTATED                                  0     0
  DNMT3A WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED                           1    10
  DNMT3A WILD-TYPE                        82   653
D28V12, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     1               82
  WHITE                                        10              653
[1] 4 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
  DNMT3A MUTATED     1   9
  DNMT3A WILD-TYPE  35 546
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    9
  DNMT3A WILD-TYPE   35  546
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  1               35
  NOT HISPANIC OR LATINO              9              546
[1] 2 2
[1] FALSE

Clustering(29) Variable = KIAA0922 MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  KIAA0922 MUTATED     5   2
  KIAA0922 WILD-TYPE 573 200
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 7                773 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 2                200 
$`KIAA0922 MUTATED`
TCGA-2Z-A9JS TCGA-Y8-A898 TCGA-A3-3313 TCGA-CW-6090 TCGA-2Z-A9JE TCGA-B1-A656 
       16.18        15.62        24.16        83.90        56.81        20.32 
TCGA-DZ-6132 
       80.88 

$`KIAA0922 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A8RZ TCGA-KL-8323 
       62.83        86.37        21.60        15.91         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3317 
      105.60        96.62        90.48        92.55        39.16        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         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-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       79.86        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             15.62               0.07 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             83.90             194.79 
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
             24.16              37.02 
[1] "15.6 - 83.9 (24.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.1"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA0922 MUTATED         7        0         0        0
  KIAA0922 WILD-TYPE     392       89       175       93
D29V3, multiclass
           clus
vv          KIAA0922 MUTATED KIAA0922 WILD-TYPE
  STAGE I                  7                392
  STAGE II                 0                 89
  STAGE III                0                175
  STAGE IV                 0                 93
[1] 4 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
  KIAA0922 MUTATED     7   0   0   0
  KIAA0922 WILD-TYPE 416 111 237  11
D29V4, multiclass
    clus
vv   KIAA0922 MUTATED KIAA0922 WILD-TYPE
  T1                7                416
  T2                0                111
  T3                0                237
  T4                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA0922 MUTATED     2   0   0
  KIAA0922 WILD-TYPE 291  40   5
D29V5, multiclass
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 2                336 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KN-8430 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A3-3358         TCGA-AK-3425         TCGA-AK-3450 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5691         TCGA-B0-5694 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5698         TCGA-B8-4621 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4158         TCGA-BP-4160         TCGA-BP-4331 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4342         TCGA-BP-4795         TCGA-BP-4799 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4986         TCGA-BP-4988         TCGA-BP-4995 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-5006         TCGA-BP-5191         TCGA-BP-5199 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-5201         TCGA-CJ-4636         TCGA-CJ-4891 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4894         TCGA-CJ-4904         TCGA-CJ-6030 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-5P-A9JU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A5Y1         TCGA-B1-A47O         TCGA-B1-A657 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5892         TCGA-BQ-7056 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A83W         TCGA-Y8-A8RZ         TCGA-KL-8326 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8327         TCGA-KL-8329         TCGA-KL-8330 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8331         TCGA-KL-8332         TCGA-KL-8333 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8334         TCGA-KL-8335         TCGA-KL-8336 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8337         TCGA-KL-8338         TCGA-KL-8340 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8443         TCGA-KN-8418 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KO-8405         TCGA-KO-8406         TCGA-KO-8407 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-KO-8410 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KO-8413         TCGA-KO-8414         TCGA-KO-8415 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KO-8416         TCGA-KO-8417         TCGA-A3-3317 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A3-3331         TCGA-A3-3347         TCGA-A3-3349 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A3-3357         TCGA-A3-3362         TCGA-A3-3367 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A3-3370         TCGA-A3-3373         TCGA-A3-3374 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A3-3376         TCGA-A3-3385         TCGA-A3-3387 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3428         TCGA-AK-3429 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AK-3430         TCGA-AK-3436         TCGA-AK-3443 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AK-3451         TCGA-AK-3456         TCGA-B0-4690 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4691         TCGA-B0-4693         TCGA-B0-4703 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4810         TCGA-B0-4811 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4814         TCGA-B0-4816         TCGA-B0-4817 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4823         TCGA-B0-4824         TCGA-B0-4827 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4833         TCGA-B0-4837         TCGA-B0-4838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4839         TCGA-B0-4842         TCGA-B0-4843 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-4846         TCGA-B0-4852         TCGA-B0-4945 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5075         TCGA-B0-5077         TCGA-B0-5080 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5081         TCGA-B0-5083         TCGA-B0-5084 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5085         TCGA-B0-5092         TCGA-B0-5094 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5095         TCGA-B0-5096         TCGA-B0-5097 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5104         TCGA-B0-5106         TCGA-B0-5107 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5108         TCGA-B0-5109         TCGA-B0-5110 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5113         TCGA-B0-5115         TCGA-B0-5116 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5119         TCGA-B0-5120         TCGA-B0-5121 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5692 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5699 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5701         TCGA-B0-5702         TCGA-B0-5703 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5705         TCGA-B0-5706         TCGA-B0-5707 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B0-5710         TCGA-B0-5712         TCGA-B0-5713 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B2-5633         TCGA-B2-5641         TCGA-B4-5377 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5844         TCGA-B8-4143         TCGA-B8-4148 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-4620         TCGA-B8-4622         TCGA-B8-5158 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-5159         TCGA-B8-5163         TCGA-B8-5164 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-5165         TCGA-B8-5545         TCGA-B8-5546 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-5553         TCGA-BP-4159         TCGA-BP-4162 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4165         TCGA-BP-4166 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4169         TCGA-BP-4170         TCGA-BP-4173 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4174         TCGA-BP-4326         TCGA-BP-4329 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4330         TCGA-BP-4337         TCGA-BP-4338 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4340         TCGA-BP-4343         TCGA-BP-4345 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4346         TCGA-BP-4351         TCGA-BP-4352 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4354         TCGA-BP-4756         TCGA-BP-4761 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4768         TCGA-BP-4770         TCGA-BP-4771 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4787         TCGA-BP-4797         TCGA-BP-4798 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4960         TCGA-BP-4964         TCGA-BP-4967 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4968         TCGA-BP-4970         TCGA-BP-4971 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-4974         TCGA-BP-4985         TCGA-BP-4989 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-5007         TCGA-BP-5010         TCGA-BP-5169 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BP-5182         TCGA-BP-5186         TCGA-BP-5198 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4638         TCGA-CJ-4639         TCGA-CJ-4640 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4643         TCGA-CJ-4644         TCGA-CJ-4868 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4869         TCGA-CJ-4872         TCGA-CJ-4873 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4874         TCGA-CJ-4876         TCGA-CJ-4890 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-4892         TCGA-CJ-4900         TCGA-CJ-4918 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CJ-5678         TCGA-CJ-6033         TCGA-CW-5585 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CW-5591         TCGA-CW-6087         TCGA-CZ-4857 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-4859         TCGA-CZ-4863         TCGA-CZ-5451 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5454         TCGA-CZ-5456 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5469         TCGA-CZ-5470 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5988         TCGA-CZ-5989         TCGA-2Z-A9J1 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93X 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-7583         TCGA-A4-7585 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-A57E         TCGA-A4-A7UZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A655 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5889 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5893 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-DW-7963 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DZ-6131         TCGA-F9-A8NY         TCGA-F9-A97G 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LD         TCGA-GL-6846 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-GL-7966         TCGA-GL-A59R         TCGA-GL-A9DC 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-J7-6720 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-J7-8537         TCGA-J7-A8I2         TCGA-KV-A74V 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-A5E8         TCGA-P4-A5EA 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-P4-AAVL         TCGA-SX-A71R         TCGA-SX-A7SM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SS         TCGA-UN-AAZ9 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PX         TCGA-Y8-A897 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
D29V6, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED     3   0
  KIAA0922 WILD-TYPE 491  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      3    0
  KIAA0922 WILD-TYPE  491   81
   clus
vv  KIAA0922 MUTATED KIAA0922 WILD-TYPE
  0                3                491
  1                0                 81
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  KIAA0922 MUTATED     0   7
  KIAA0922 WILD-TYPE 258 519
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      0    7
  KIAA0922 WILD-TYPE  258  519
        clus
vv       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  FEMALE                0                258
  MALE                  7                519
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "KIAA0922 MUTATED"      
clus
  KIAA0922 MUTATED KIAA0922 WILD-TYPE 
                 1                125 
        TCGA-KM-8439         TCGA-KM-8441         TCGA-KM-8442 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KO-8411         TCGA-CZ-4854         TCGA-CZ-4856 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-4862         TCGA-DV-5565         TCGA-DV-5566 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DV-5568         TCGA-DV-5569         TCGA-DV-5574 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-2Z-A9JL 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JT         TCGA-5P-A9JU         TCGA-DW-5560 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A71W         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8440         TCGA-KM-8443 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KM-8639 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-KN-8429         TCGA-KN-8434         TCGA-KO-8413 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-AK-3428         TCGA-AK-3430         TCGA-B0-4838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5832         TCGA-B4-5834 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4861         TCGA-CZ-5456 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5457         TCGA-CZ-5458         TCGA-CZ-5465 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-EU-5904 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JN         TCGA-4A-A93W 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-A4-7286 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-7828         TCGA-A4-8098         TCGA-A4-8310 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8517 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A4ZT         TCGA-A4-A57E         TCGA-A4-A5DU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A6HP         TCGA-AL-3466 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-DW-7963         TCGA-EV-5901         TCGA-EV-5902 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A7Q0         TCGA-G7-6789 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A71S         TCGA-SX-A71U 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A71V         TCGA-SX-A7SL         TCGA-SX-A7SM 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SN         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
        TCGA-UZ-A9PL         TCGA-V9-A7HT 
"KIAA0922 WILD-TYPE" "KIAA0922 WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KIAA0922 MUTATED                    0                                 2
  KIAA0922 WILD-TYPE                 66                               434
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KIAA0922 MUTATED                                       5
  KIAA0922 WILD-TYPE                                   277
D29V9, multiclass
                                       clus
vv                                      KIAA0922 MUTATED KIAA0922 WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                    2                434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                5                277
[1] 3 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
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA0922 MUTATED                                  0     0
  KIAA0922 WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA0922 MUTATED                           1     5
  KIAA0922 WILD-TYPE                        82   658
D29V12, multiclass
                                  clus
vv                                 KIAA0922 MUTATED KIAA0922 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 14
  BLACK OR AFRICAN AMERICAN                       1                 82
  WHITE                                           5                658
[1] 4 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
  KIAA0922 MUTATED     0   4
  KIAA0922 WILD-TYPE  36 551
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA0922 MUTATED      0    4
  KIAA0922 WILD-TYPE   36  551
                        clus
vv                       KIAA0922 MUTATED KIAA0922 WILD-TYPE
  HISPANIC OR LATINO                    0                 36
  NOT HISPANIC OR LATINO                4                551
[1] 2 2
[1] FALSE

Clustering(30) Variable = GPR50 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 575 200
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             775 
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             200 
$`GPR50 MUTATED`
TCGA-DV-5575 TCGA-DV-5576 TCGA-PJ-A5Z9 TCGA-KN-8436 TCGA-B0-4817 
       56.84        23.90        17.75        42.35        33.50 

$`GPR50 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       11.67        66.28        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       19.73        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       45.07        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  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           37.02 
[1] "17.8 - 56.8 (33.5)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.9"
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GPR50 MUTATED         3        1         1        0
  GPR50 WILD-TYPE     396       88       174       93
D30V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE I               3             396
  STAGE II              1              88
  STAGE III             1             174
  STAGE IV              0              93
[1] 4 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 420 110 236  11
D30V4, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  T1             3             420
  T2             1             110
  T3             1             236
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR50 MUTATED     1   0   0
  GPR50 WILD-TYPE 292  40   5
D30V5, multiclass
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1             337 
     TCGA-KL-8328      TCGA-KL-8339      TCGA-KN-8430      TCGA-A3-3358 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3450      TCGA-B0-5088      TCGA-B0-5691 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5698      TCGA-B8-4621 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4160      TCGA-BP-4331      TCGA-BP-4342 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4799      TCGA-BP-4986      TCGA-BP-4988 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5191      TCGA-BP-5199 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4891      TCGA-CJ-4894 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-6030      TCGA-CZ-4854      TCGA-CZ-4856 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-KL-8326      TCGA-KL-8327      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-8340      TCGA-KL-8341      TCGA-KL-8342 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418      TCGA-KN-8419 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423      TCGA-KN-8424 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8410      TCGA-KO-8413      TCGA-KO-8414 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8415      TCGA-KO-8416      TCGA-KO-8417      TCGA-A3-3313 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347      TCGA-A3-3349 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3357      TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3373      TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3387      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-3451 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691      TCGA-B0-4693 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810      TCGA-B0-4811 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4823      TCGA-B0-4824 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5085      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5699 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      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-B8-4148      TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4620      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4159      TCGA-BP-4162      TCGA-BP-4163 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4330      TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4960      TCGA-BP-4964 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4989      TCGA-BP-5007 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5198      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4890      TCGA-CJ-4892      TCGA-CJ-4900      TCGA-CJ-4918 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CW-6087      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93X 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466      TCGA-AL-3472 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-F9-A8NY      TCGA-F9-A97G      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-G7-A8LD      TCGA-GL-6846 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KV-A74V      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-P4-AAVL      TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Y8-A897 
"GPR50 WILD-TYPE" 
D30V6, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   0
  GPR50 WILD-TYPE 491  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    0
  GPR50 WILD-TYPE  491   81
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3             491
  1             0              81
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 255 524
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    2
  GPR50 WILD-TYPE  255  524
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             3             255
  MALE               2             524
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             124 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU      TCGA-DW-5560 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836      TCGA-DW-7837 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO      TCGA-UZ-A9PZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443      TCGA-KM-8476 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429      TCGA-KN-8434 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430      TCGA-B0-4838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286      TCGA-A4-7828 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0      TCGA-G7-6789 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL      TCGA-V9-A7HT 
"GPR50 WILD-TYPE" "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                                   281
D30V9, 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             281
[1] 3 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:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              93 
     TCGA-B8-4621      TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-IZ-A6M8      TCGA-PJ-A8JU      TCGA-SX-A71W 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ      TCGA-KL-8324 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     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-8428      TCGA-KN-8433      TCGA-KO-8408 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445      TCGA-AK-3451 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4146      TCGA-B8-5158      TCGA-B8-5164      TCGA-B8-5550 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9J2      TCGA-2Z-A9J5      TCGA-2Z-A9J7      TCGA-2Z-A9J8 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9JI      TCGA-2Z-A9JK      TCGA-2Z-A9JM      TCGA-2Z-A9JN 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-5P-A9K3 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-5P-A9KE      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G 
"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-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-GL-7773 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A83S      TCGA-IA-A83V      TCGA-MH-A854 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-MH-A856      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-Y8-A894      TCGA-Y8-A896 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Y8-A8RY 
"GPR50 WILD-TYPE" 
D30V11, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A8JU      TCGA-SX-A71W 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ      TCGA-KL-8330 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345      TCGA-KM-8639 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409      TCGA-AK-3445 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550      TCGA-2Z-A9J3 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-A4-A48D 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472      TCGA-AL-7173 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR50 MUTATED                                  0     0
  GPR50 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED                           1     4
  GPR50 WILD-TYPE                        82   659
D30V12, multiclass
                                  clus
vv                                 GPR50 MUTATED GPR50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                        4             659
[1] 4 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
  GPR50 MUTATED     0   5
  GPR50 WILD-TYPE  36 550
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    5
  GPR50 WILD-TYPE   36  550
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             5             550
[1] 2 2
[1] FALSE

Clustering(31) Variable = ACSF2 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  ACSF2 MUTATED     5   6
  ACSF2 WILD-TYPE 573 196
  ACSF2 MUTATED ACSF2 WILD-TYPE 
             11             769 
  ACSF2 MUTATED ACSF2 WILD-TYPE 
              6             196 
$`ACSF2 MUTATED`
TCGA-DV-5576 TCGA-2Z-A9JS TCGA-IA-A83W TCGA-B0-4828 TCGA-B0-5092 TCGA-BP-4787 
       23.90        16.18        67.17        10.09        15.09        15.78 
TCGA-BP-4970 TCGA-CZ-5459 TCGA-A4-8098 TCGA-B9-A5W8 TCGA-UZ-A9PL 
       14.24        55.33        29.46        17.23       103.63 

$`ACSF2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       11.67        66.28        56.84        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       25.58        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       17.95        84.89        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       14.93        54.48        29.10        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 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-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
        7.30        25.32        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 
       10.82         5.33        61.97        56.91        68.38        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       57.40        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       91.69        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      117.40       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  ACSF2 MUTATED ACSF2 WILD-TYPE 
          10.09            0.07 
  ACSF2 MUTATED ACSF2 WILD-TYPE 
         103.63          194.79 
  ACSF2 MUTATED ACSF2 WILD-TYPE 
          17.23           37.25 
[1] "10.1 - 103.6 (17.2)" "0.1 - 194.8 (37.2)" 
[1] "hr=" "2.8"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ACSF2 MUTATED         4        2         2        3
  ACSF2 WILD-TYPE     395       87       173       90
D31V3, multiclass
           clus
vv          ACSF2 MUTATED ACSF2 WILD-TYPE
  STAGE I               4             395
  STAGE II              2              87
  STAGE III             2             173
  STAGE IV              3              90
[1] 4 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
  ACSF2 MUTATED     6   3   2   0
  ACSF2 WILD-TYPE 417 108 235  11
D31V4, multiclass
    clus
vv   ACSF2 MUTATED ACSF2 WILD-TYPE
  T1             6             417
  T2             3             108
  T3             2             235
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ACSF2 MUTATED     3   1   0
  ACSF2 WILD-TYPE 290  39   5
D31V5, multiclass
    clus
vv   ACSF2 MUTATED ACSF2 WILD-TYPE
  N0             3             290
  N1             1              39
  N2             0               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"
D31V6, binary
                 cls
clus                0   1
  ACSF2 MUTATED     5   3
  ACSF2 WILD-TYPE 489  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSF2 MUTATED      5    3
  ACSF2 WILD-TYPE  489   78
   clus
vv  ACSF2 MUTATED ACSF2 WILD-TYPE
  0             5             489
  1             3              78
[1] 2 2
[1] FALSE
D31V7, binary
                 cls
clus                0   1
  ACSF2 MUTATED     3   8
  ACSF2 WILD-TYPE 255 518
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSF2 MUTATED      3    8
  ACSF2 WILD-TYPE  255  518
        clus
vv       ACSF2 MUTATED ACSF2 WILD-TYPE
  FEMALE             3             255
  MALE               8             518
[1] 2 2
[1] FALSE
D31V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ACSF2 MUTATED                    0                                 6
  ACSF2 WILD-TYPE                 66                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ACSF2 MUTATED                                       5
  ACSF2 WILD-TYPE                                   277
D31V9, multiclass
                                       clus
vv                                      ACSF2 MUTATED ACSF2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             5             277
[1] 3 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
  ACSF2 MUTATED                                  0     1
  ACSF2 WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ACSF2 MUTATED                           3     7
  ACSF2 WILD-TYPE                        80   656
D31V12, multiclass
                                  clus
vv                                 ACSF2 MUTATED ACSF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    3              80
  WHITE                                        7             656
[1] 4 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
  ACSF2 MUTATED     0   8
  ACSF2 WILD-TYPE  36 547
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACSF2 MUTATED      0    8
  ACSF2 WILD-TYPE   36  547
                        clus
vv                       ACSF2 MUTATED ACSF2 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             8             547
[1] 2 2
[1] FALSE

Clustering(32) Variable = WDR52 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  WDR52 MUTATED     6   3
  WDR52 WILD-TYPE 572 199
  WDR52 MUTATED WDR52 WILD-TYPE 
              9             771 
  WDR52 MUTATED WDR52 WILD-TYPE 
              3             199 
$`WDR52 MUTATED`
TCGA-B0-4712 TCGA-2Z-A9JL TCGA-BQ-7056 TCGA-KN-8421 TCGA-B0-4811 TCGA-B0-5117 
       43.96        33.07        20.12        87.91        46.59        52.87 
TCGA-B2-4101 TCGA-CJ-4637 TCGA-MH-A55W 
       21.30        73.22        34.29 

$`WDR52 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ 
       66.28        56.84        23.90        34.85        39.88        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       13.25        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33       129.37        23.47        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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
        1.68        31.96        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 
       19.82        34.95         0.95       115.00        46.55        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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       11.41        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  WDR52 MUTATED WDR52 WILD-TYPE 
          20.12            0.07 
  WDR52 MUTATED WDR52 WILD-TYPE 
          87.91          194.79 
  WDR52 MUTATED WDR52 WILD-TYPE 
          43.96           36.95 
[1] "20.1 - 87.9 (44.0)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.2"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  WDR52 MUTATED         3        2         2        2
  WDR52 WILD-TYPE     396       87       173       91
D32V3, multiclass
           clus
vv          WDR52 MUTATED WDR52 WILD-TYPE
  STAGE I               3             396
  STAGE II              2              87
  STAGE III             2             173
  STAGE IV              2              91
[1] 4 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
  WDR52 MUTATED     3   3   3   0
  WDR52 WILD-TYPE 420 108 234  11
D32V4, multiclass
    clus
vv   WDR52 MUTATED WDR52 WILD-TYPE
  T1             3             420
  T2             3             108
  T3             3             234
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  WDR52 MUTATED     3   0   0
  WDR52 WILD-TYPE 290  40   5
D32V5, multiclass
    clus
vv   WDR52 MUTATED WDR52 WILD-TYPE
  N0             3             290
  N1             0              40
  N2             0               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"
D32V6, binary
                 cls
clus                0   1
  WDR52 MUTATED     4   2
  WDR52 WILD-TYPE 490  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR52 MUTATED      4    2
  WDR52 WILD-TYPE  490   79
   clus
vv  WDR52 MUTATED WDR52 WILD-TYPE
  0             4             490
  1             2              79
[1] 2 2
[1] FALSE
D32V7, binary
                 cls
clus                0   1
  WDR52 MUTATED     3   6
  WDR52 WILD-TYPE 255 520
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR52 MUTATED      3    6
  WDR52 WILD-TYPE  255  520
        clus
vv       WDR52 MUTATED WDR52 WILD-TYPE
  FEMALE             3             255
  MALE               6             520
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "WDR52 MUTATED"         
clus
  WDR52 MUTATED WDR52 WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JT      TCGA-5P-A9JU 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL 
"WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" "WDR52 WILD-TYPE" 
     TCGA-V9-A7HT 
"WDR52 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  WDR52 MUTATED                    1                                 5
  WDR52 WILD-TYPE                 65                               431
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  WDR52 MUTATED                                       3
  WDR52 WILD-TYPE                                   279
D32V9, multiclass
                                       clus
vv                                      WDR52 MUTATED WDR52 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             279
[1] 3 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
  WDR52 MUTATED                                  0     0
  WDR52 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  WDR52 MUTATED                           2     7
  WDR52 WILD-TYPE                        81   656
D32V12, multiclass
                                  clus
vv                                 WDR52 MUTATED WDR52 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    2              81
  WHITE                                        7             656
[1] 4 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
  WDR52 MUTATED     1   8
  WDR52 WILD-TYPE  35 547
[1] "tbl2"
                 cls
clus              [,1] [,2]
  WDR52 MUTATED      1    8
  WDR52 WILD-TYPE   35  547
                        clus
vv                       WDR52 MUTATED WDR52 WILD-TYPE
  HISPANIC OR LATINO                 1              35
  NOT HISPANIC OR LATINO             8             547
[1] 2 2
[1] FALSE

Clustering(33) Variable = ALMS1 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  ALMS1 MUTATED    12   2
  ALMS1 WILD-TYPE 566 200
  ALMS1 MUTATED ALMS1 WILD-TYPE 
             14             766 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              2             200 
$`ALMS1 MUTATED`
TCGA-BP-4999 TCGA-BP-5201 TCGA-5P-A9JV TCGA-B0-5120 TCGA-B0-5696 TCGA-BP-4960 
       41.62        31.27        67.17        38.43        85.78        71.41 
TCGA-CJ-4918 TCGA-GL-A9DE TCGA-HE-A5NJ TCGA-J7-A8I2 TCGA-P4-AAVM TCGA-UZ-A9PL 
        3.06        16.31        56.75        10.09        50.60       103.63 
TCGA-UZ-A9PU TCGA-Y8-A896 
       30.67        18.64 

$`ALMS1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.79        44.55        63.25        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       16.18        22.49        12.26        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 
       38.63        52.73        41.88        52.87        51.02        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 
       46.39        56.98        42.41       129.67        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       47.97        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 
       49.28        50.33        54.48        38.56        45.14         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.43        12.89        11.21        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       92.58        16.01        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9PX 
      125.29        37.35        98.96        71.24        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  ALMS1 MUTATED ALMS1 WILD-TYPE 
           3.06            0.07 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
         103.63          194.79 
  ALMS1 MUTATED ALMS1 WILD-TYPE 
         40.025          36.950 
[1] "3.1 - 103.6 (40.0)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.9"
D33V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ALMS1 MUTATED         6        2         2        2
  ALMS1 WILD-TYPE     393       87       173       91
D33V3, multiclass
           clus
vv          ALMS1 MUTATED ALMS1 WILD-TYPE
  STAGE I               6             393
  STAGE II              2              87
  STAGE III             2             173
  STAGE IV              2              91
[1] 4 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
  ALMS1 MUTATED     8   2   4   0
  ALMS1 WILD-TYPE 415 109 233  11
D33V4, multiclass
    clus
vv   ALMS1 MUTATED ALMS1 WILD-TYPE
  T1             8             415
  T2             2             109
  T3             4             233
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  ALMS1 MUTATED     6   0   0
  ALMS1 WILD-TYPE 287  40   5
D33V5, multiclass
    clus
vv   ALMS1 MUTATED ALMS1 WILD-TYPE
  N0             6             287
  N1             0              40
  N2             0               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"
D33V6, binary
                 cls
clus                0   1
  ALMS1 MUTATED     6   2
  ALMS1 WILD-TYPE 488  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      6    2
  ALMS1 WILD-TYPE  488   79
   clus
vv  ALMS1 MUTATED ALMS1 WILD-TYPE
  0             6             488
  1             2              79
[1] 2 2
[1] FALSE
D33V7, binary
                 cls
clus                0   1
  ALMS1 MUTATED     1  13
  ALMS1 WILD-TYPE 257 513
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      1   13
  ALMS1 WILD-TYPE  257  513
        clus
vv       ALMS1 MUTATED ALMS1 WILD-TYPE
  FEMALE             1             257
  MALE              13             513
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-7836      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SO      TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B8-5158      TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-EU-5906      TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-F9-A7Q0      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A8LC      TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71R      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SL      TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SQ      TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-V9-A7HT 
"ALMS1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ALMS1 MUTATED                    0                                 6
  ALMS1 WILD-TYPE                 66                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ALMS1 MUTATED                                       8
  ALMS1 WILD-TYPE                                   274
D33V9, multiclass
                                       clus
vv                                      ALMS1 MUTATED ALMS1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             8             274
[1] 3 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
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              2              92 
     TCGA-B8-4621      TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-IZ-A6M8      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-5158      TCGA-B8-5164 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B8-5550      TCGA-2Z-A9J2      TCGA-2Z-A9J5      TCGA-2Z-A9J7 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JK      TCGA-2Z-A9JM 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-5P-A9K3      TCGA-5P-A9KE      TCGA-A4-8310      TCGA-A4-A48D 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-7963 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-F9-A97G      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-HE-A5NK 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A83S      TCGA-IA-A83V      TCGA-MH-A854 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-MH-A856      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-Y8-A894      TCGA-Y8-A8RY 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
D33V11, continuous
[1] "Remove cluster labels:" "ALMS1 MUTATED"         
clus
  ALMS1 MUTATED ALMS1 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Q2-A5QZ      TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-UZ-A9PS      TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
     TCGA-Y8-A894      TCGA-Y8-A8RY 
"ALMS1 WILD-TYPE" "ALMS1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALMS1 MUTATED                                  0     1
  ALMS1 WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  ALMS1 MUTATED                           1    11
  ALMS1 WILD-TYPE                        82   652
D33V12, multiclass
                                  clus
vv                                 ALMS1 MUTATED ALMS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                       11             652
[1] 4 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
  ALMS1 MUTATED     2  10
  ALMS1 WILD-TYPE  34 545
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ALMS1 MUTATED      2   10
  ALMS1 WILD-TYPE   34  545
                        clus
vv                       ALMS1 MUTATED ALMS1 WILD-TYPE
  HISPANIC OR LATINO                 2              34
  NOT HISPANIC OR LATINO            10             545
[1] 2 2
[1] FALSE

Clustering(34) Variable = TXNIP MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  TXNIP MUTATED     6   2
  TXNIP WILD-TYPE 572 200
  TXNIP MUTATED TXNIP WILD-TYPE 
              8             772 
  TXNIP MUTATED TXNIP WILD-TYPE 
              2             200 
$`TXNIP MUTATED`
TCGA-BP-5201 TCGA-B0-4810 TCGA-CJ-4869 TCGA-CJ-5684 TCGA-CZ-4866 TCGA-5P-A9K8 
       31.27        15.72        83.97        73.35       107.41        43.04 
TCGA-BQ-5889 TCGA-HE-7130 
       10.82        58.19 

$`TXNIP WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        44.55        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-5686 TCGA-CJ-6028 
       25.25        18.15       122.83        62.10        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       63.39        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9KA TCGA-5P-A9KC 
       22.26        78.64        15.48        62.93        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  TXNIP MUTATED TXNIP WILD-TYPE 
          10.82            0.07 
  TXNIP MUTATED TXNIP WILD-TYPE 
         107.41          194.79 
  TXNIP MUTATED TXNIP WILD-TYPE 
         50.615          36.950 
[1] "10.8 - 107.4 (50.6)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1.2"
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TXNIP MUTATED         1        0         4        2
  TXNIP WILD-TYPE     398       89       171       91
D34V3, multiclass
           clus
vv          TXNIP MUTATED TXNIP WILD-TYPE
  STAGE I               1             398
  STAGE II              0              89
  STAGE III             4             171
  STAGE IV              2              91
[1] 4 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
  TXNIP MUTATED     1   1   6   0
  TXNIP WILD-TYPE 422 110 231  11
D34V4, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  T1             1             422
  T2             1             110
  T3             6             231
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TXNIP MUTATED     1   3   0
  TXNIP WILD-TYPE 292  37   5
D34V5, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  N0             1             292
  N1             3              37
  N2             0               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"
D34V6, binary
                 cls
clus                0   1
  TXNIP MUTATED     5   2
  TXNIP WILD-TYPE 489  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      5    2
  TXNIP WILD-TYPE  489   79
   clus
vv  TXNIP MUTATED TXNIP WILD-TYPE
  0             5             489
  1             2              79
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus                0   1
  TXNIP MUTATED     3   5
  TXNIP WILD-TYPE 255 521
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      3    5
  TXNIP WILD-TYPE  255  521
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  FEMALE             3             255
  MALE               5             521
[1] 2 2
[1] FALSE
D34V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TXNIP MUTATED                    0                                 5
  TXNIP WILD-TYPE                 66                               431
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TXNIP MUTATED                                       3
  TXNIP WILD-TYPE                                   279
D34V9, multiclass
                                       clus
vv                                      TXNIP MUTATED TXNIP WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             279
[1] 3 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
  TXNIP MUTATED                                  0     0
  TXNIP WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TXNIP MUTATED                           0     7
  TXNIP WILD-TYPE                        83   656
D34V12, multiclass
                                  clus
vv                                 TXNIP MUTATED TXNIP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    0              83
  WHITE                                        7             656
[1] 4 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
  TXNIP MUTATED     1   6
  TXNIP WILD-TYPE  35 549
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      1    6
  TXNIP WILD-TYPE   35  549
                        clus
vv                       TXNIP MUTATED TXNIP WILD-TYPE
  HISPANIC OR LATINO                 1              35
  NOT HISPANIC OR LATINO             6             549
[1] 2 2
[1] FALSE

Clustering(35) Variable = NUDT11 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  NUDT11 MUTATED     5   0
  NUDT11 WILD-TYPE 573 202
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               5              775 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               0              202 
$`NUDT11 MUTATED`
TCGA-DW-7839 TCGA-B4-5838 TCGA-B8-4153 TCGA-BP-5195 TCGA-BP-5202 
       13.78         5.46        25.05        24.62         0.95 

$`NUDT11 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       16.80        49.97        42.71        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 
       23.47        13.41        33.47        19.82        34.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  NUDT11 MUTATED NUDT11 WILD-TYPE 
            0.95             0.07 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           25.05           194.79 
  NUDT11 MUTATED NUDT11 WILD-TYPE 
           13.78            37.25 
[1] "0.9 - 25.1 (13.8)"  "0.1 - 194.8 (37.2)"
[1] "hr="     "1200000"
D35V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NUDT11 MUTATED         2        0         2        1
  NUDT11 WILD-TYPE     397       89       173       92
D35V3, multiclass
           clus
vv          NUDT11 MUTATED NUDT11 WILD-TYPE
  STAGE I                2              397
  STAGE II               0               89
  STAGE III              2              173
  STAGE IV               1               92
[1] 4 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 421 111 234  11
D35V4, multiclass
    clus
vv   NUDT11 MUTATED NUDT11 WILD-TYPE
  T1              2              421
  T2              0              111
  T3              3              234
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NUDT11 MUTATED     0   1   0
  NUDT11 WILD-TYPE 293  39   5
D35V5, multiclass
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               1              337 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4904       TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-KL-8326       TCGA-KL-8327       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-8340       TCGA-KL-8341       TCGA-KL-8342 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3373       TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A3-3387       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-3451 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5400       TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4162       TCGA-BP-4163 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4960       TCGA-BP-4964 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4989       TCGA-BP-5007 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BP-5198       TCGA-CJ-4638       TCGA-CJ-4639       TCGA-CJ-4640 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874       TCGA-CJ-4876 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-4890       TCGA-CJ-4892       TCGA-CJ-4900       TCGA-CJ-4918 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6033       TCGA-CW-5585       TCGA-CW-5591 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CW-6087       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       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-G7-A8LD       TCGA-GL-6846 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-Y8-A897 
"NUDT11 WILD-TYPE" 
D35V6, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     4   0
  NUDT11 WILD-TYPE 490  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      4    0
  NUDT11 WILD-TYPE  490   81
   clus
vv  NUDT11 MUTATED NUDT11 WILD-TYPE
  0              4              490
  1              0               81
[1] 2 2
[1] FALSE
D35V7, binary
                  cls
clus                 0   1
  NUDT11 MUTATED     1   4
  NUDT11 WILD-TYPE 257 522
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      1    4
  NUDT11 WILD-TYPE  257  522
        clus
vv       NUDT11 MUTATED NUDT11 WILD-TYPE
  FEMALE              1              257
  MALE                4              522
[1] 2 2
[1] FALSE
D35V8, continuous
[1] "Remove cluster labels:" "NUDT11 MUTATED"        
clus
  NUDT11 MUTATED NUDT11 WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7840 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440       TCGA-KM-8443 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639       TCGA-KN-8429 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428       TCGA-AK-3430 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5843       TCGA-B4-5844 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158       TCGA-CJ-6028 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-5456       TCGA-CZ-5457 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN       TCGA-4A-A93W 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286       TCGA-A4-7828 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963       TCGA-EV-5901 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0       TCGA-G7-6789 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71S 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" "NUDT11 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"NUDT11 WILD-TYPE" "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                                   281
D35V9, 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              281
[1] 3 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
  NUDT11 MUTATED                                  0     0
  NUDT11 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NUDT11 MUTATED                           0     5
  NUDT11 WILD-TYPE                        83   658
D35V12, multiclass
                                  clus
vv                                 NUDT11 MUTATED NUDT11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         5              658
[1] 4 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
  NUDT11 MUTATED     0   4
  NUDT11 WILD-TYPE  36 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NUDT11 MUTATED      0    4
  NUDT11 WILD-TYPE   36  551
                        clus
vv                       NUDT11 MUTATED NUDT11 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(36) Variable = PCK1 MUTATION ANALYSIS
D36V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     6   3
  PCK1 WILD-TYPE 572 199
  PCK1 MUTATED PCK1 WILD-TYPE 
             9            771 
  PCK1 MUTATED PCK1 WILD-TYPE 
             3            199 
$`PCK1 MUTATED`
TCGA-2Z-A9JS TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 TCGA-AL-3472 
       16.18        37.38       109.41        51.02        49.97        66.71 
TCGA-G7-A8LB TCGA-SX-A7SP TCGA-UZ-A9PJ 
       17.98        16.31        26.20 

$`PCK1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        52.87        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        47.67        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 
       15.75         8.28        12.46         9.63        70.19        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         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-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
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-G7-A8LC TCGA-G7-A8LD 
       25.15        20.52        25.84        25.25        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       11.93        19.00        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  PCK1 MUTATED PCK1 WILD-TYPE 
         16.18           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
        109.41         194.79 
  PCK1 MUTATED PCK1 WILD-TYPE 
         37.38          36.95 
[1] "16.2 - 109.4 (37.4)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1.3"
D36V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         5        1         1        1
  PCK1 WILD-TYPE     394       88       174       92
D36V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              5            394
  STAGE II             1             88
  STAGE III            1            174
  STAGE IV             1             92
[1] 4 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     5   3   1   0
  PCK1 WILD-TYPE 418 108 236  11
D36V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            5            418
  T2            3            108
  T3            1            236
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PCK1 MUTATED     4   0   0
  PCK1 WILD-TYPE 289  40   5
D36V5, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  N0            4            289
  N1            0             40
  N2            0              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"
D36V6, binary
                cls
clus               0   1
  PCK1 MUTATED     6   0
  PCK1 WILD-TYPE 488  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      6    0
  PCK1 WILD-TYPE  488   81
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            6            488
  1            0             81
[1] 2 2
[1] FALSE
D36V7, binary
                cls
clus               0   1
  PCK1 MUTATED     3   6
  PCK1 WILD-TYPE 255 520
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      3    6
  PCK1 WILD-TYPE  255  520
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            3            255
  MALE              6            520
[1] 2 2
[1] FALSE
D36V8, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             2            124 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7836     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4622 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-EU-5904     TCGA-EU-5905 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-EU-5906     TCGA-EU-5907     TCGA-2Z-A9JE     TCGA-2Z-A9JK 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-G7-A8LC 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SQ     TCGA-SX-A7SR 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
                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                                       5
  PCK1 WILD-TYPE                                   277
D36V9, multiclass
                                       clus
vv                                      PCK1 MUTATED PCK1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                4            432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            277
[1] 3 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:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             2             92 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    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-B8-5158     TCGA-B8-5164 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-5550     TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-5P-A9K3     TCGA-5P-A9KE     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-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854     TCGA-MH-A856 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896     TCGA-Y8-A8RY 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
D36V11, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             2             65 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    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-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"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-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-MH-A854 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ     TCGA-SX-A71S 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM     TCGA-SX-A7SR 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS     TCGA-UZ-A9PX 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894     TCGA-Y8-A896 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-Y8-A8RY 
"PCK1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCK1 MUTATED                                  0     0
  PCK1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED                           1     8
  PCK1 WILD-TYPE                        82   655
D36V12, multiclass
                                  clus
vv                                 PCK1 MUTATED PCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   1             82
  WHITE                                       8            655
[1] 4 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
  PCK1 MUTATED     0   8
  PCK1 WILD-TYPE  36 547
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    8
  PCK1 WILD-TYPE   36  547
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            8            547
[1] 2 2
[1] FALSE

Clustering(37) Variable = RAI1 MUTATION ANALYSIS
D37V1, survival
                sevent
clus2              0   1
  RAI1 MUTATED     8   3
  RAI1 WILD-TYPE 570 199
  RAI1 MUTATED RAI1 WILD-TYPE 
            11            769 
  RAI1 MUTATED RAI1 WILD-TYPE 
             3            199 
$`RAI1 MUTATED`
TCGA-CJ-4904 TCGA-DV-5575 TCGA-5P-A9JV TCGA-KN-8431 TCGA-KO-8404 TCGA-B0-5077 
      108.56        56.84        67.17        19.33        10.68        43.30 
TCGA-2Z-A9J6 TCGA-5P-A9K6 TCGA-A4-8630 TCGA-IA-A83S TCGA-UZ-A9Q1 
       56.91        62.93        14.33        85.78        51.35 

$`RAI1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       27.65       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       66.28        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       16.18        22.49        12.26        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       20.94        11.24        11.90        34.36         7.30        25.32 
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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22       100.27         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       15.48        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A48D TCGA-A4-A4ZT 
       23.28        23.31        19.63        19.73        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-A9G9 
       30.67        47.47        65.13       110.73        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  RAI1 MUTATED RAI1 WILD-TYPE 
         10.68           0.07 
  RAI1 MUTATED RAI1 WILD-TYPE 
        108.56         194.79 
  RAI1 MUTATED RAI1 WILD-TYPE 
         56.84          36.85 
[1] "10.7 - 108.6 (56.8)" "0.1 - 194.8 (36.9)" 
[1] "hr=" "1.2"
D37V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RAI1 MUTATED         5        1         0        2
  RAI1 WILD-TYPE     394       88       175       91
D37V3, multiclass
           clus
vv          RAI1 MUTATED RAI1 WILD-TYPE
  STAGE I              5            394
  STAGE II             1             88
  STAGE III            0            175
  STAGE IV             2             91
[1] 4 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     7   1   1   1
  RAI1 WILD-TYPE 416 110 236  10
D37V4, multiclass
    clus
vv   RAI1 MUTATED RAI1 WILD-TYPE
  T1            7            416
  T2            1            110
  T3            1            236
  T4            1             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
  RAI1 MUTATED     2   0   0
  RAI1 WILD-TYPE 291  40   5
D37V5, multiclass
[1] "Remove cluster labels:" "RAI1 MUTATED"          
clus
  RAI1 MUTATED RAI1 WILD-TYPE 
             2            336 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-5P-A9JU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657     TCGA-BQ-5888 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W     TCGA-Y8-A8RZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8329     TCGA-KL-8330 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333     TCGA-KL-8334 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337     TCGA-KL-8338 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342     TCGA-KL-8343 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346     TCGA-KM-8438 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419     TCGA-KN-8421 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424     TCGA-KN-8425 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429     TCGA-KO-8405 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313     TCGA-A3-3317 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3357 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385     TCGA-A3-3387 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429     TCGA-AK-3430 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3451     TCGA-AK-3456 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693     TCGA-B0-4703 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4814 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823     TCGA-B0-4824 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837     TCGA-B0-4838 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843     TCGA-B0-4846 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075     TCGA-B0-5080 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5081     TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5692 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5699     TCGA-B0-5701 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159     TCGA-B8-5163 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545     TCGA-B8-5546 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5553 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4165 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170     TCGA-BP-4173 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329     TCGA-BP-4330 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4343 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4797 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964     TCGA-BP-4967 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4974 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007     TCGA-BP-5010 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186     TCGA-BP-5198 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918     TCGA-CJ-5678 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-2Z-A9J1 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5893 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131     TCGA-F9-A8NY 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846     TCGA-GL-7966 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U     TCGA-IA-A40Y 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2     TCGA-KV-A74V 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-AAVL 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP     TCGA-SX-A7SS 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX     TCGA-Y8-A897 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
D37V6, binary
                cls
clus               0   1
  RAI1 MUTATED     2   1
  RAI1 WILD-TYPE 492  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      2    1
  RAI1 WILD-TYPE  492   80
   clus
vv  RAI1 MUTATED RAI1 WILD-TYPE
  0            2            492
  1            1             80
[1] 2 2
[1] FALSE
D37V7, binary
                cls
clus               0   1
  RAI1 MUTATED     5   6
  RAI1 WILD-TYPE 253 520
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      5    6
  RAI1 WILD-TYPE  253  520
        clus
vv       RAI1 MUTATED RAI1 WILD-TYPE
  FEMALE            5            253
  MALE              6            520
[1] 2 2
[1] FALSE
D37V8, continuous
[1] "Remove cluster labels:" "RAI1 MUTATED"          
clus
  RAI1 MUTATED RAI1 WILD-TYPE 
             2            124 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT     TCGA-5P-A9JU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7836 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W     TCGA-SX-A7SO 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440     TCGA-KM-8443 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639     TCGA-KN-8429 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428     TCGA-AK-3430 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4622     TCGA-B8-5158 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-5456 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465     TCGA-CZ-5469 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-CZ-5982     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-EU-5907     TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-2Z-A9JN 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-A48D 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-7963     TCGA-EV-5901 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A7Q0     TCGA-G7-6789 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC     TCGA-G7-A8LD 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R     TCGA-SX-A71S 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL     TCGA-SX-A7SM 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A7SN     TCGA-SX-A7SP     TCGA-SX-A7SQ     TCGA-SX-A7SR 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL     TCGA-V9-A7HT 
"RAI1 WILD-TYPE" "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                                       6
  RAI1 WILD-TYPE                                   276
D37V9, multiclass
                                       clus
vv                                      RAI1 MUTATED RAI1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                3            433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            6            276
[1] 3 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
[1] "Remove cluster labels:" "RAI1 MUTATED"          
clus
  RAI1 MUTATED RAI1 WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B8-5550     TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-5P-A9K3     TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IA-A83V     TCGA-MH-A854 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896 
"RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" "RAI1 WILD-TYPE" 
    TCGA-Y8-A8RY 
"RAI1 WILD-TYPE" 
D37V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RAI1 MUTATED                                  0     0
  RAI1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RAI1 MUTATED                           0    10
  RAI1 WILD-TYPE                        83   653
D37V12, multiclass
                                  clus
vv                                 RAI1 MUTATED RAI1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                      10            653
[1] 4 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
  RAI1 MUTATED     0  10
  RAI1 WILD-TYPE  36 545
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAI1 MUTATED      0   10
  RAI1 WILD-TYPE   36  545
                        clus
vv                       RAI1 MUTATED RAI1 WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO           10            545
[1] 2 2
[1] FALSE

Clustering(38) Variable = PAM MUTATION ANALYSIS
D38V1, survival
               sevent
clus2             0   1
  PAM MUTATED     4   0
  PAM WILD-TYPE 574 202
  PAM MUTATED PAM WILD-TYPE 
            4           776 
  PAM MUTATED PAM WILD-TYPE 
            0           202 
$`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-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 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-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y 
       26.01        56.75        73.25        25.22        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       31.13        15.48        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  PAM MUTATED PAM WILD-TYPE 
        11.84          0.07 
  PAM MUTATED PAM WILD-TYPE 
       123.09        194.79 
  PAM MUTATED PAM WILD-TYPE 
       58.290        36.985 
[1] "11.8 - 123.1 (58.3)" "0.1 - 194.8 (37.0)" 
[1] "hr="     "3300000"
D38V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         2        0         2        0
  PAM WILD-TYPE     397       89       173       93
D38V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             2           397
  STAGE II            0            89
  STAGE III           2           173
  STAGE IV            0            93
[1] 4 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 420 111 236  11
D38V4, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  T1           3           420
  T2           0           111
  T3           1           236
  T4           0            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  PAM MUTATED     2   1   0
  PAM WILD-TYPE 291  39   5
D38V5, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  N0           2           291
  N1           1            39
  N2           0             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"
D38V6, binary
               cls
clus              0   1
  PAM MUTATED     2   0
  PAM WILD-TYPE 492  81
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      2    0
  PAM WILD-TYPE  492   81
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           2           492
  1           0            81
[1] 2 2
[1] FALSE
D38V7, binary
               cls
clus              0   1
  PAM MUTATED     1   3
  PAM WILD-TYPE 257 523
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      1    3
  PAM WILD-TYPE  257  523
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           1           257
  MALE             3           523
[1] 2 2
[1] FALSE
D38V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1           125 
   TCGA-KM-8439    TCGA-KM-8441    TCGA-KM-8442    TCGA-KO-8411    TCGA-CZ-4854 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-4856    TCGA-CZ-4862    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-2Z-A9JL 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JT    TCGA-5P-A9JU    TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7836    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-SX-A71W    TCGA-SX-A7SO    TCGA-UZ-A9PZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8438    TCGA-KM-8440    TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8429    TCGA-KN-8434    TCGA-KO-8413    TCGA-AK-3428 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832    TCGA-B4-5834 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843    TCGA-B4-5844 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B8-4143    TCGA-B8-4622    TCGA-B8-5158    TCGA-CJ-6028    TCGA-CZ-4858 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-4861    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5458    TCGA-CZ-5465 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-5469    TCGA-CZ-5982    TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5906 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EU-5907    TCGA-2Z-A9JE    TCGA-2Z-A9JK    TCGA-2Z-A9JN    TCGA-4A-A93W 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8098 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312    TCGA-A4-8517    TCGA-A4-8518 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8630    TCGA-A4-A48D    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-7963    TCGA-EV-5901 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-F9-A7Q0    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-G7-A8LB    TCGA-G7-A8LC 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-IA-A40X    TCGA-IA-A40Y    TCGA-J7-8537 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Q2-A5QZ    TCGA-SX-A71R    TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A71V 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SN    TCGA-SX-A7SP    TCGA-SX-A7SQ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-SX-A7SU    TCGA-UZ-A9PL    TCGA-V9-A7HT 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "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                                   279
D38V9, 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           279
[1] 3 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
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            92 
   TCGA-B8-4621    TCGA-2Z-A9JD    TCGA-2Z-A9JQ    TCGA-5P-A9JU    TCGA-B9-A44B 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-GL-A59T    TCGA-IZ-A6M8 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-PJ-A5Z9    TCGA-PJ-A8JU    TCGA-SX-A71W    TCGA-UZ-A9PO    TCGA-UZ-A9PR 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A8RZ    TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KO-8409    TCGA-KO-8416    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-4146 
"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-2Z-A9J2    TCGA-2Z-A9J5 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JK    TCGA-2Z-A9JM 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-2Z-A9JN    TCGA-2Z-A9JO    TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-5P-A9K3 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-5P-A9KE    TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A69E    TCGA-DW-7963 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-F9-A97G    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-G7-A8LB    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-7773    TCGA-GL-A9DD 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A83S    TCGA-IA-A83V    TCGA-MH-A854 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-MH-A856    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-Q2-A5QZ    TCGA-SX-A71S 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-SX-A71U    TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SR    TCGA-SX-A7SS 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-UZ-A9PM    TCGA-UZ-A9PS    TCGA-UZ-A9PX    TCGA-WN-A9G9    TCGA-Y8-A894 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-Y8-A896    TCGA-Y8-A8RY 
"PAM WILD-TYPE" "PAM WILD-TYPE" 
D38V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2    14
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     2
  PAM WILD-TYPE                        82   661
D38V12, multiclass
                                  clus
vv                                 PAM MUTATED PAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            14
  BLACK OR AFRICAN AMERICAN                  1            82
  WHITE                                      2           661
[1] 4 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
  PAM MUTATED     0   3
  PAM WILD-TYPE  36 552
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   36  552
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0            36
  NOT HISPANIC OR LATINO           3           552
[1] 2 2
[1] FALSE

Clustering(39) Variable = KDM6A MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     9   4
  KDM6A WILD-TYPE 569 198
  KDM6A MUTATED KDM6A WILD-TYPE 
             13             767 
  KDM6A MUTATED KDM6A WILD-TYPE 
              4             198 
$`KDM6A MUTATED`
TCGA-A4-7584 TCGA-BQ-5886 TCGA-B0-5075 TCGA-B2-4098 TCGA-CZ-5465 TCGA-5P-A9K0 
       21.37        26.04        20.94         1.68        84.30        22.26 
TCGA-5P-A9KE TCGA-A4-A48D TCGA-HE-7129 TCGA-HE-7130 TCGA-J7-A8I2 TCGA-SX-A7SP 
       27.09        12.46        81.93        58.19        10.09        16.31 
TCGA-SX-A7SS 
       53.10 

$`KDM6A WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
        2.27        36.85        70.52        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       91.46        32.61        35.90        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.89        11.21        16.31        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        27.06        11.93        19.00        41.62        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  KDM6A MUTATED KDM6A WILD-TYPE 
           1.68            0.07 
  KDM6A MUTATED KDM6A WILD-TYPE 
          84.30          194.79 
  KDM6A MUTATED KDM6A WILD-TYPE 
          22.26           37.25 
[1] "1.7 - 84.3 (22.3)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "1.5"
D39V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         6        1         4        0
  KDM6A WILD-TYPE     393       88       171       93
D39V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               6             393
  STAGE II              1              88
  STAGE III             4             171
  STAGE IV              0              93
[1] 4 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     8   1   4   0
  KDM6A WILD-TYPE 415 110 233  11
D39V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             8             415
  T2             1             110
  T3             4             233
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM6A MUTATED     4   0   0
  KDM6A WILD-TYPE 289  40   5
D39V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0             4             289
  N1             0              40
  N2             0               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"
D39V6, binary
                 cls
clus                0   1
  KDM6A MUTATED    10   0
  KDM6A WILD-TYPE 484  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED     10    0
  KDM6A WILD-TYPE  484   81
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0            10             484
  1             0              81
[1] 2 2
[1] FALSE
D39V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     5   8
  KDM6A WILD-TYPE 253 518
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      5    8
  KDM6A WILD-TYPE  253  518
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             5             253
  MALE               8             518
[1] 2 2
[1] FALSE
D39V8, continuous
                 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                                      10
  KDM6A WILD-TYPE                                   272
D39V9, multiclass
                                       clus
vv                                      KDM6A MUTATED KDM6A WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            10             272
[1] 3 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
D39V11, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              65 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     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-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"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-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-UZ-A9PM      TCGA-UZ-A9PS      TCGA-UZ-A9PX 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894      TCGA-Y8-A896 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-Y8-A8RY 
"KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  0     1
  KDM6A WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           3     6
  KDM6A WILD-TYPE                        80   657
D39V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    3              80
  WHITE                                        6             657
[1] 4 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
  KDM6A MUTATED     0   9
  KDM6A WILD-TYPE  36 546
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    9
  KDM6A WILD-TYPE   36  546
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             9             546
[1] 2 2
[1] FALSE

Clustering(40) Variable = GLS MUTATION ANALYSIS
D40V1, survival
               sevent
clus2             0   1
  GLS MUTATED     7   2
  GLS WILD-TYPE 571 200
  GLS MUTATED GLS WILD-TYPE 
            9           771 
  GLS MUTATED GLS WILD-TYPE 
            2           200 
$`GLS MUTATED`
TCGA-BP-4775 TCGA-PJ-A5Z8 TCGA-PJ-A8JU TCGA-KN-8436 TCGA-B0-4828 TCGA-CZ-5984 
       60.59        19.73        12.49        42.35        10.09        67.96 
TCGA-2Z-A9JP TCGA-B9-4617 TCGA-P4-A5E8 
       29.36         1.15        42.94 

$`GLS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       44.15        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        17.75        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 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-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98        42.41       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       80.91        71.41        73.84       149.16       105.37       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       31.10        12.69        80.19        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       30.71        24.33        31.20         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        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-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       17.62        31.13        15.48        99.78        87.09         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  GLS MUTATED GLS WILD-TYPE 
         1.15          0.07 
  GLS MUTATED GLS WILD-TYPE 
        67.96        194.79 
  GLS MUTATED GLS WILD-TYPE 
        29.36         37.02 
[1] "1.1 - 68.0 (29.4)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "1.2"
D40V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  GLS MUTATED         5        1         1        1
  GLS WILD-TYPE     394       88       174       92
D40V3, multiclass
           clus
vv          GLS MUTATED GLS WILD-TYPE
  STAGE I             5           394
  STAGE II            1            88
  STAGE III           1           174
  STAGE IV            1            92
[1] 4 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
  GLS MUTATED     6   3   0   0
  GLS WILD-TYPE 417 108 237  11
D40V4, multiclass
    clus
vv   GLS MUTATED GLS WILD-TYPE
  T1           6           417
  T2           3           108
  T3           0           237
  T4           0            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  GLS MUTATED     1   1   0
  GLS WILD-TYPE 292  39   5
D40V5, multiclass
[1] "Remove cluster labels:" "GLS MUTATED"           
clus
  GLS MUTATED GLS WILD-TYPE 
            2           336 
   TCGA-KL-8328    TCGA-KL-8339    TCGA-KN-8430    TCGA-A3-3358    TCGA-AK-3425 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AK-3450    TCGA-B0-5088    TCGA-B0-5691    TCGA-B0-5694    TCGA-B0-5695 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5698    TCGA-B8-4621    TCGA-BP-4158    TCGA-BP-4160    TCGA-BP-4331 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4342    TCGA-BP-4795    TCGA-BP-4799    TCGA-BP-4986    TCGA-BP-4988 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4995    TCGA-BP-5006    TCGA-BP-5191    TCGA-BP-5199    TCGA-BP-5201 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CJ-4636    TCGA-CJ-4891    TCGA-CJ-4894    TCGA-CJ-4904    TCGA-CJ-6030 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CZ-4854    TCGA-CZ-4856    TCGA-5P-A9JU    TCGA-A4-A5Y1    TCGA-B1-A47O 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B1-A657    TCGA-BQ-5888    TCGA-BQ-5892    TCGA-BQ-7056    TCGA-IA-A83W 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-Y8-A8RZ    TCGA-KL-8326    TCGA-KL-8327    TCGA-KL-8329    TCGA-KL-8330 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KL-8331    TCGA-KL-8332    TCGA-KL-8333    TCGA-KL-8334    TCGA-KL-8335 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KL-8336    TCGA-KL-8337    TCGA-KL-8338    TCGA-KL-8340    TCGA-KL-8341 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KL-8342    TCGA-KL-8343    TCGA-KL-8344    TCGA-KL-8345    TCGA-KL-8346 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KM-8438    TCGA-KM-8443    TCGA-KN-8418    TCGA-KN-8419    TCGA-KN-8421 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KN-8422    TCGA-KN-8423    TCGA-KN-8424    TCGA-KN-8425    TCGA-KN-8427 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KN-8428    TCGA-KN-8429    TCGA-KO-8405    TCGA-KO-8406    TCGA-KO-8407 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KO-8408    TCGA-KO-8409    TCGA-KO-8410    TCGA-KO-8413    TCGA-KO-8414 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KO-8415    TCGA-KO-8416    TCGA-KO-8417    TCGA-A3-3313    TCGA-A3-3317 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-A3-3331    TCGA-A3-3347    TCGA-A3-3349    TCGA-A3-3357    TCGA-A3-3362 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-A3-3367    TCGA-A3-3370    TCGA-A3-3373    TCGA-A3-3374    TCGA-A3-3376 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-A3-3385    TCGA-A3-3387    TCGA-AK-3427    TCGA-AK-3428    TCGA-AK-3429 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AK-3430    TCGA-AK-3436    TCGA-AK-3443    TCGA-AK-3451    TCGA-AK-3456 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-4690    TCGA-B0-4691    TCGA-B0-4693    TCGA-B0-4703    TCGA-B0-4710 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-4810    TCGA-B0-4811    TCGA-B0-4814    TCGA-B0-4816    TCGA-B0-4817 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-4823    TCGA-B0-4824    TCGA-B0-4827    TCGA-B0-4833    TCGA-B0-4837 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-4838    TCGA-B0-4839    TCGA-B0-4842    TCGA-B0-4843    TCGA-B0-4846 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-4852    TCGA-B0-4945    TCGA-B0-5075    TCGA-B0-5077    TCGA-B0-5080 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5081    TCGA-B0-5083    TCGA-B0-5084    TCGA-B0-5085    TCGA-B0-5092 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5094    TCGA-B0-5095    TCGA-B0-5096    TCGA-B0-5097    TCGA-B0-5104 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5106    TCGA-B0-5107    TCGA-B0-5108    TCGA-B0-5109    TCGA-B0-5110 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5113    TCGA-B0-5115    TCGA-B0-5116    TCGA-B0-5119    TCGA-B0-5120 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5121    TCGA-B0-5399    TCGA-B0-5400    TCGA-B0-5692    TCGA-B0-5696 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5697    TCGA-B0-5699    TCGA-B0-5701    TCGA-B0-5702    TCGA-B0-5703 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5705    TCGA-B0-5706    TCGA-B0-5707    TCGA-B0-5710    TCGA-B0-5712 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B0-5713    TCGA-B2-5633    TCGA-B2-5641    TCGA-B4-5377    TCGA-B4-5832 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B4-5844    TCGA-B8-4143    TCGA-B8-4148    TCGA-B8-4151    TCGA-B8-4154 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B8-4619    TCGA-B8-4620    TCGA-B8-4622    TCGA-B8-5158    TCGA-B8-5159 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B8-5163    TCGA-B8-5164    TCGA-B8-5165    TCGA-B8-5545    TCGA-B8-5546 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B8-5549    TCGA-B8-5550    TCGA-B8-5551    TCGA-B8-5553    TCGA-BP-4159 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4162    TCGA-BP-4163    TCGA-BP-4165    TCGA-BP-4166    TCGA-BP-4169 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4170    TCGA-BP-4173    TCGA-BP-4174    TCGA-BP-4326    TCGA-BP-4329 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4330    TCGA-BP-4337    TCGA-BP-4338    TCGA-BP-4340    TCGA-BP-4343 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4345    TCGA-BP-4346    TCGA-BP-4351    TCGA-BP-4352    TCGA-BP-4354 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4756    TCGA-BP-4761    TCGA-BP-4768    TCGA-BP-4770    TCGA-BP-4771 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4787    TCGA-BP-4797    TCGA-BP-4798    TCGA-BP-4960    TCGA-BP-4964 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4967    TCGA-BP-4968    TCGA-BP-4970    TCGA-BP-4971    TCGA-BP-4974 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-4985    TCGA-BP-4989    TCGA-BP-5007    TCGA-BP-5010    TCGA-BP-5169 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BP-5182    TCGA-BP-5186    TCGA-BP-5198    TCGA-CJ-4638    TCGA-CJ-4639 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CJ-4640    TCGA-CJ-4643    TCGA-CJ-4644    TCGA-CJ-4868    TCGA-CJ-4869 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CJ-4872    TCGA-CJ-4873    TCGA-CJ-4874    TCGA-CJ-4876    TCGA-CJ-4890 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CJ-4892    TCGA-CJ-4900    TCGA-CJ-4918    TCGA-CJ-5678    TCGA-CJ-6033 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CW-5585    TCGA-CW-5591    TCGA-CW-6087    TCGA-CZ-4857    TCGA-CZ-4859 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CZ-4863    TCGA-CZ-5451    TCGA-CZ-5452    TCGA-CZ-5454    TCGA-CZ-5456 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CZ-5467    TCGA-CZ-5469    TCGA-CZ-5470    TCGA-CZ-5985    TCGA-CZ-5986 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-CZ-5988    TCGA-CZ-5989    TCGA-2Z-A9J1    TCGA-2Z-A9JO    TCGA-4A-A93W 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-4A-A93X    TCGA-4A-A93Y    TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7915 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A7UZ    TCGA-AL-3466    TCGA-AL-3472    TCGA-AL-3473 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AL-7173    TCGA-B1-5398    TCGA-B1-A655    TCGA-B1-A656    TCGA-B9-7268 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880    TCGA-BQ-5882 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5889    TCGA-BQ-5890    TCGA-BQ-5891 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-BQ-7051    TCGA-DW-7963    TCGA-DZ-6131    TCGA-F9-A8NY    TCGA-F9-A97G 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-G7-6789    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-G7-A8LD 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-A59R    TCGA-GL-A9DC    TCGA-IA-A40U 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-6720    TCGA-J7-8537    TCGA-J7-A8I2    TCGA-KV-A74V 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-P4-A5E6    TCGA-P4-A5EA    TCGA-P4-AAVL    TCGA-SX-A71R    TCGA-SX-A7SM 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-SX-A7SP    TCGA-SX-A7SS    TCGA-UN-AAZ9    TCGA-UZ-A9PM    TCGA-UZ-A9PX 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-Y8-A897 
"GLS WILD-TYPE" 
D40V6, binary
               cls
clus              0   1
  GLS MUTATED     5   1
  GLS WILD-TYPE 489  80
[1] "tbl2"
               cls
clus            [,1] [,2]
  GLS MUTATED      5    1
  GLS WILD-TYPE  489   80
   clus
vv  GLS MUTATED GLS WILD-TYPE
  0           5           489
  1           1            80
[1] 2 2
[1] FALSE
D40V7, binary
               cls
clus              0   1
  GLS MUTATED     3   6
  GLS WILD-TYPE 255 520
[1] "tbl2"
               cls
clus            [,1] [,2]
  GLS MUTATED      3    6
  GLS WILD-TYPE  255  520
        clus
vv       GLS MUTATED GLS WILD-TYPE
  FEMALE           3           255
  MALE             6           520
[1] 2 2
[1] FALSE
D40V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GLS MUTATED                    1                                 3
  GLS WILD-TYPE                 65                               433
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GLS MUTATED                                       5
  GLS WILD-TYPE                                   277
D40V9, multiclass
                                       clus
vv                                      GLS MUTATED GLS WILD-TYPE
  KIDNEY CHROMOPHOBE                              1            65
  KIDNEY CLEAR CELL RENAL CARCINOMA               3           433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           5           277
[1] 3 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:" "GLS MUTATED"           
clus
  GLS MUTATED GLS WILD-TYPE 
            1            93 
   TCGA-B8-4621    TCGA-2Z-A9JD    TCGA-2Z-A9JQ    TCGA-5P-A9JU    TCGA-B9-A44B 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7838    TCGA-GL-A59T    TCGA-IZ-A6M8 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-PJ-A5Z9    TCGA-SX-A71W    TCGA-UZ-A9PO    TCGA-UZ-A9PR    TCGA-Y8-A8RZ 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KO-8416    TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-4146    TCGA-B8-5158 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B8-5164    TCGA-B8-5550    TCGA-2Z-A9J2    TCGA-2Z-A9J5    TCGA-2Z-A9J7 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JK    TCGA-2Z-A9JM    TCGA-2Z-A9JN 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-2Z-A9JO    TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-5P-A9K3    TCGA-5P-A9KE 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-A4-8310    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4115 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-G7-6792    TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-7501    TCGA-G7-A8LB 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-7773    TCGA-GL-A9DD    TCGA-HE-A5NI 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U    TCGA-IA-A83S    TCGA-IA-A83V 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-MH-A854    TCGA-MH-A856    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-Q2-A5QZ 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A7SL    TCGA-SX-A7SM    TCGA-SX-A7SR 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-SX-A7SS    TCGA-UZ-A9PM    TCGA-UZ-A9PS    TCGA-UZ-A9PX    TCGA-WN-A9G9 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-Y8-A894    TCGA-Y8-A896    TCGA-Y8-A8RY 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
D40V11, continuous
[1] "Remove cluster labels:" "GLS MUTATED"           
clus
  GLS MUTATED GLS WILD-TYPE 
            1            66 
   TCGA-2Z-A9JD    TCGA-DW-5561    TCGA-PJ-A5Z9    TCGA-SX-A71W    TCGA-UZ-A9PO 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-UZ-A9PR    TCGA-Y8-A8RZ    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AK-3445    TCGA-AK-3451    TCGA-B8-5158    TCGA-B8-5550    TCGA-2Z-A9J3 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-2Z-A9J7    TCGA-2Z-A9J8    TCGA-2Z-A9JI    TCGA-2Z-A9JN    TCGA-2Z-A9JO 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-4A-A93W    TCGA-4A-A93Y    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4114    TCGA-B9-4117 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-7963    TCGA-F9-A97G    TCGA-G7-6793    TCGA-G7-6795 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-A8LB    TCGA-G7-A8LD    TCGA-G7-A8LE    TCGA-GL-7773 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-GL-A9DD    TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-MH-A854    TCGA-MH-A856 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-P4-A5E6    TCGA-Q2-A5QZ    TCGA-SX-A71S    TCGA-SX-A71U    TCGA-SX-A7SL 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-SX-A7SM    TCGA-SX-A7SR    TCGA-SX-A7SS    TCGA-UZ-A9PM    TCGA-UZ-A9PS 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-UZ-A9PX    TCGA-WN-A9G9    TCGA-WN-AB4C    TCGA-Y8-A894    TCGA-Y8-A896 
"GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" "GLS WILD-TYPE" 
   TCGA-Y8-A8RY 
"GLS WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GLS MUTATED                                  0     0
  GLS WILD-TYPE                                2    14
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  GLS MUTATED                           1     8
  GLS WILD-TYPE                        82   655
D40V12, multiclass
                                  clus
vv                                 GLS MUTATED GLS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            14
  BLACK OR AFRICAN AMERICAN                  1            82
  WHITE                                      8           655
[1] 4 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
  GLS MUTATED     0   7
  GLS WILD-TYPE  36 548
[1] "tbl2"
               cls
clus            [,1] [,2]
  GLS MUTATED      0    7
  GLS WILD-TYPE   36  548
                        clus
vv                       GLS MUTATED GLS WILD-TYPE
  HISPANIC OR LATINO               0            36
  NOT HISPANIC OR LATINO           7           548
[1] 2 2
[1] FALSE

Clustering(41) Variable = EPS15L1 MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  EPS15L1 MUTATED     7   3
  EPS15L1 WILD-TYPE 571 199
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
               10               770 
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
                3               199 
$`EPS15L1 MUTATED`
TCGA-BP-4986 TCGA-B9-5155 TCGA-B9-A44B TCGA-KL-8333 TCGA-A3-3313 TCGA-B0-5097 
       25.81        21.86        11.87        98.33        24.16        21.86 
TCGA-BP-4330 TCGA-BP-4341 TCGA-BQ-7044 TCGA-IA-A83T 
       62.07        52.24       123.62        88.24 

$`EPS15L1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       61.51        53.65        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       27.68        21.07        10.16        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.75        12.49        35.38        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        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-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       90.48        92.55        39.16        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4345 
       27.78         0.07        93.99        18.48        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       10.82         7.66         0.95         7.92         2.76        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       85.78        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
            11.87              0.07 
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
           123.62            194.79 
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
           39.025            36.985 
[1] "11.9 - 123.6 (39.0)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  EPS15L1 MUTATED         2        1         6        0
  EPS15L1 WILD-TYPE     397       88       169       93
D41V3, multiclass
           clus
vv          EPS15L1 MUTATED EPS15L1 WILD-TYPE
  STAGE I                 2               397
  STAGE II                1                88
  STAGE III               6               169
  STAGE IV                0                93
[1] 4 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
  EPS15L1 MUTATED     2   1   6   0
  EPS15L1 WILD-TYPE 421 110 231  11
D41V4, multiclass
    clus
vv   EPS15L1 MUTATED EPS15L1 WILD-TYPE
  T1               2               421
  T2               1               110
  T3               6               231
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  EPS15L1 MUTATED     5   0   0
  EPS15L1 WILD-TYPE 288  40   5
D41V5, multiclass
    clus
vv   EPS15L1 MUTATED EPS15L1 WILD-TYPE
  N0               5               288
  N1               0                40
  N2               0                 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"
D41V6, binary
                   cls
clus                  0   1
  EPS15L1 MUTATED     7   0
  EPS15L1 WILD-TYPE 487  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPS15L1 MUTATED      7    0
  EPS15L1 WILD-TYPE  487   81
   clus
vv  EPS15L1 MUTATED EPS15L1 WILD-TYPE
  0               7               487
  1               0                81
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  EPS15L1 MUTATED     2   8
  EPS15L1 WILD-TYPE 256 518
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPS15L1 MUTATED      2    8
  EPS15L1 WILD-TYPE  256  518
        clus
vv       EPS15L1 MUTATED EPS15L1 WILD-TYPE
  FEMALE               2               256
  MALE                 8               518
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  EPS15L1 MUTATED                    1                                 5
  EPS15L1 WILD-TYPE                 65                               431
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  EPS15L1 MUTATED                                       4
  EPS15L1 WILD-TYPE                                   278
D41V9, multiclass
                                       clus
vv                                      EPS15L1 MUTATED EPS15L1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   5               431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               4               278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
[1] "Remove cluster labels:" "EPS15L1 MUTATED"       
clus
  EPS15L1 MUTATED EPS15L1 WILD-TYPE 
                1                93 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU        TCGA-SX-A71W 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-KL-8324 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445        TCGA-AK-3451 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" "EPS15L1 WILD-TYPE" 
       TCGA-Y8-A8RY 
"EPS15L1 WILD-TYPE" 
D41V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPS15L1 MUTATED                                  0     0
  EPS15L1 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  EPS15L1 MUTATED                           3     7
  EPS15L1 WILD-TYPE                        80   656
D41V12, multiclass
                                  clus
vv                                 EPS15L1 MUTATED EPS15L1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      3                80
  WHITE                                          7               656
[1] 4 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
  EPS15L1 MUTATED     2   4
  EPS15L1 WILD-TYPE  34 551
[1] "tbl2"
                   cls
clus                [,1] [,2]
  EPS15L1 MUTATED      2    4
  EPS15L1 WILD-TYPE   34  551
                        clus
vv                       EPS15L1 MUTATED EPS15L1 WILD-TYPE
  HISPANIC OR LATINO                   2                34
  NOT HISPANIC OR LATINO               4               551
[1] 2 2
[1] FALSE

Clustering(42) Variable = NOM1 MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  NOM1 MUTATED     6   0
  NOM1 WILD-TYPE 572 202
  NOM1 MUTATED NOM1 WILD-TYPE 
             6            774 
  NOM1 MUTATED NOM1 WILD-TYPE 
             0            202 
$`NOM1 MUTATED`
TCGA-Y8-A8RZ TCGA-KN-8427 TCGA-CJ-5683 TCGA-CZ-4863 TCGA-CZ-5988 TCGA-BQ-7062 
        6.74         0.99        62.10        63.39        22.78         3.81 

$`NOM1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25        18.15       122.83        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       14.66       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-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-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 
       50.40        49.84         7.63         7.04         7.17        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
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-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  NOM1 MUTATED NOM1 WILD-TYPE 
          0.99           0.07 
  NOM1 MUTATED NOM1 WILD-TYPE 
         63.39         194.79 
  NOM1 MUTATED NOM1 WILD-TYPE 
         14.76          37.12 
[1] "1.0 - 63.4 (14.8)"  "0.1 - 194.8 (37.1)"
[1] "hr="     "3300000"
D42V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NOM1 MUTATED         4        0         1        1
  NOM1 WILD-TYPE     395       89       174       92
D42V3, multiclass
           clus
vv          NOM1 MUTATED NOM1 WILD-TYPE
  STAGE I              4            395
  STAGE II             0             89
  STAGE III            1            174
  STAGE IV             1             92
[1] 4 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
  NOM1 MUTATED     4   0   1   1
  NOM1 WILD-TYPE 419 111 236  10
D42V4, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  T1            4            419
  T2            0            111
  T3            1            236
  T4            1             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
  NOM1 MUTATED     3   1   0
  NOM1 WILD-TYPE 290  39   5
D42V5, multiclass
    clus
vv   NOM1 MUTATED NOM1 WILD-TYPE
  N0            3            290
  N1            1             39
  N2            0              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"
D42V6, binary
                cls
clus               0   1
  NOM1 MUTATED     4   0
  NOM1 WILD-TYPE 490  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      4    0
  NOM1 WILD-TYPE  490   81
   clus
vv  NOM1 MUTATED NOM1 WILD-TYPE
  0            4            490
  1            0             81
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus               0   1
  NOM1 MUTATED     1   5
  NOM1 WILD-TYPE 257 521
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      1    5
  NOM1 WILD-TYPE  257  521
        clus
vv       NOM1 MUTATED NOM1 WILD-TYPE
  FEMALE            1            257
  MALE              5            521
[1] 2 2
[1] FALSE
D42V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NOM1 MUTATED                    1                                 3
  NOM1 WILD-TYPE                 65                               433
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NOM1 MUTATED                                       2
  NOM1 WILD-TYPE                                   280
D42V9, multiclass
                                       clus
vv                                      NOM1 MUTATED NOM1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                3            433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            280
[1] 3 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
[1] "Remove cluster labels:" "NOM1 MUTATED"          
clus
  NOM1 MUTATED NOM1 WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-KL-8324 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433     TCGA-KO-8408 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445     TCGA-AK-3451 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164     TCGA-B8-5550 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4117 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-Y8-A8RY 
"NOM1 WILD-TYPE" 
D42V11, continuous
[1] "Remove cluster labels:" "NOM1 MUTATED"          
clus
  NOM1 MUTATED NOM1 WILD-TYPE 
             1             66 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-KL-8330 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345     TCGA-KM-8639 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409     TCGA-AK-3445 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550     TCGA-2Z-A9J3 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JN 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-A4-A48D 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472     TCGA-AL-7173 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117     TCGA-B9-A69E 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"NOM1 WILD-TYPE" "NOM1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NOM1 MUTATED                                  0     0
  NOM1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NOM1 MUTATED                           1     5
  NOM1 WILD-TYPE                        82   658
D42V12, multiclass
                                  clus
vv                                 NOM1 MUTATED NOM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   1             82
  WHITE                                       5            658
[1] 4 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
  NOM1 MUTATED     0   4
  NOM1 WILD-TYPE  36 551
[1] "tbl2"
                cls
clus             [,1] [,2]
  NOM1 MUTATED      0    4
  NOM1 WILD-TYPE   36  551
                        clus
vv                       NOM1 MUTATED NOM1 WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            4            551
[1] 2 2
[1] FALSE

Clustering(43) Variable = CDK12 MUTATION ANALYSIS
D43V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     5   3
  CDK12 WILD-TYPE 573 199
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             772 
  CDK12 MUTATED CDK12 WILD-TYPE 
              3             199 
$`CDK12 MUTATED`
TCGA-B0-5693 TCGA-DW-5560 TCGA-KL-8327 TCGA-B0-5098 TCGA-B0-5706 TCGA-CJ-4881 
      133.94        48.85       137.06        52.08       105.37        66.21 
TCGA-CZ-5454 TCGA-CZ-5468 
       23.74         1.94 

$`CDK12 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5694 TCGA-B0-5695 
       43.96        52.21        18.51       112.80        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       20.12        11.28        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
      153.73        23.84       109.22        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5707 
      126.28        80.91        71.41        73.84       149.16       123.09 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 
       35.90         1.68        31.96        21.30        31.66        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
        6.38        48.53         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       63.42        58.82        79.53        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-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  CDK12 MUTATED CDK12 WILD-TYPE 
           1.94            0.07 
  CDK12 MUTATED CDK12 WILD-TYPE 
         137.06          194.79 
  CDK12 MUTATED CDK12 WILD-TYPE 
         59.145          36.900 
[1] "1.9 - 137.1 (59.1)" "0.1 - 194.8 (36.9)"
[1] "hr=" "1"  
D43V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CDK12 MUTATED         4        1         1        2
  CDK12 WILD-TYPE     395       88       174       91
D43V3, multiclass
           clus
vv          CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I               4             395
  STAGE II              1              88
  STAGE III             1             174
  STAGE IV              2              91
[1] 4 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
  CDK12 MUTATED     4   2   2   0
  CDK12 WILD-TYPE 419 109 235  11
D43V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             4             419
  T2             2             109
  T3             2             235
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDK12 MUTATED     3   0   0
  CDK12 WILD-TYPE 290  40   5
D43V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0             3             290
  N1             0              40
  N2             0               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"
D43V6, binary
                 cls
clus                0   1
  CDK12 MUTATED     6   2
  CDK12 WILD-TYPE 488  79
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      6    2
  CDK12 WILD-TYPE  488   79
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0             6             488
  1             2              79
[1] 2 2
[1] FALSE
D43V7, binary
                 cls
clus                0   1
  CDK12 MUTATED     4   4
  CDK12 WILD-TYPE 254 522
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      4    4
  CDK12 WILD-TYPE  254  522
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE             4             254
  MALE               4             522
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-V9-A7HT 
"CDK12 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CDK12 MUTATED                    1                                 6
  CDK12 WILD-TYPE                 65                               430
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CDK12 MUTATED                                       1
  CDK12 WILD-TYPE                                   281
D43V9, multiclass
                                       clus
vv                                      CDK12 MUTATED CDK12 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             281
[1] 3 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
D43V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     0
  CDK12 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           1     7
  CDK12 WILD-TYPE                        82   656
D43V12, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                        7             656
[1] 4 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
  CDK12 MUTATED     0   7
  CDK12 WILD-TYPE  36 548
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0    7
  CDK12 WILD-TYPE   36  548
                        clus
vv                       CDK12 MUTATED CDK12 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             7             548
[1] 2 2
[1] FALSE

Clustering(44) Variable = ARHGAP35 MUTATION ANALYSIS
D44V1, survival
                    sevent
clus2                  0   1
  ARHGAP35 MUTATED     7   0
  ARHGAP35 WILD-TYPE 571 202
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 7                773 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
                 0                202 
$`ARHGAP35 MUTATED`
TCGA-B0-5812 TCGA-B0-5712 TCGA-BP-4756 TCGA-BP-5169 TCGA-CJ-5682 TCGA-CZ-5985 
      126.05        89.49        12.30         6.35       122.83        65.65 
TCGA-A4-7915 
        0.23 

$`ARHGAP35 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
       70.68       119.38        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
      131.15        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       31.33        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 
       31.10        12.69        80.19        67.96        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        62.63        18.12         3.91         6.77         4.18 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        15.48        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
       19.13         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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
              0.23               0.07 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
            126.05             194.79 
  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE 
             65.65              36.95 
[1] "0.2 - 126.0 (65.7)" "0.1 - 194.8 (37.0)"
[1] "hr="     "9100000"
D44V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  ARHGAP35 MUTATED         3        2         0        2
  ARHGAP35 WILD-TYPE     396       87       175       91
D44V3, multiclass
           clus
vv          ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  STAGE I                  3                396
  STAGE II                 2                 87
  STAGE III                0                175
  STAGE IV                 2                 91
[1] 4 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 420 108 236  11
D44V4, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  T1                3                420
  T2                3                108
  T3                1                236
  T4                0                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  ARHGAP35 MUTATED     5   0   0
  ARHGAP35 WILD-TYPE 288  40   5
D44V5, multiclass
    clus
vv   ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  N0                5                288
  N1                0                 40
  N2                0                  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"
D44V6, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     4   2
  ARHGAP35 WILD-TYPE 490  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      4    2
  ARHGAP35 WILD-TYPE  490   79
   clus
vv  ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  0                4                490
  1                2                 79
[1] 2 2
[1] FALSE
D44V7, binary
                    cls
clus                   0   1
  ARHGAP35 MUTATED     3   4
  ARHGAP35 WILD-TYPE 255 522
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      3    4
  ARHGAP35 WILD-TYPE  255  522
        clus
vv       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  FEMALE                3                255
  MALE                  4                522
[1] 2 2
[1] FALSE
D44V8, 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                                   281
D44V9, 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                281
[1] 3 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
D44V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARHGAP35 MUTATED                                  0     1
  ARHGAP35 WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  ARHGAP35 MUTATED                           2     4
  ARHGAP35 WILD-TYPE                        81   659
D44V12, multiclass
                                  clus
vv                                 ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 13
  BLACK OR AFRICAN AMERICAN                       2                 81
  WHITE                                           4                659
[1] 4 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
  ARHGAP35 MUTATED     0   5
  ARHGAP35 WILD-TYPE  36 550
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  ARHGAP35 MUTATED      0    5
  ARHGAP35 WILD-TYPE   36  550
                        clus
vv                       ARHGAP35 MUTATED ARHGAP35 WILD-TYPE
  HISPANIC OR LATINO                    0                 36
  NOT HISPANIC OR LATINO                5                550
[1] 2 2
[1] FALSE

Clustering(45) Variable = RIMBP3 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     2   3
  RIMBP3 WILD-TYPE 576 199
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              775 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               3              199 
$`RIMBP3 MUTATED`
TCGA-BP-4164 TCGA-KO-8404 TCGA-KO-8409 TCGA-B0-4945 TCGA-BP-4964 
       32.61        10.68       104.55        70.52        61.22 

$`RIMBP3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
      111.02        94.72        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       59.08       115.00        42.35       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
      103.40        92.71        16.67       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       36.85        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
       66.31        78.18        74.66         1.35        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           10.68             0.07 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
          104.55           194.79 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           61.22            36.95 
[1] "10.7 - 104.5 (61.2)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1.9"
D45V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RIMBP3 MUTATED         2        1         1        1
  RIMBP3 WILD-TYPE     397       88       174       92
D45V3, multiclass
           clus
vv          RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                2              397
  STAGE II               1               88
  STAGE III              1              174
  STAGE IV               1               92
[1] 4 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 421 110 236  10
D45V4, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              2              421
  T2              1              110
  T3              1              236
  T4              1               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
  RIMBP3 MUTATED     3   0   0
  RIMBP3 WILD-TYPE 290  40   5
D45V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              3              290
  N1              0               40
  N2              0                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"
D45V6, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   0
  RIMBP3 WILD-TYPE 490  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    0
  RIMBP3 WILD-TYPE  490   81
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              4              490
  1              0               81
[1] 2 2
[1] FALSE
D45V7, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     3   2
  RIMBP3 WILD-TYPE 255 524
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      3    2
  RIMBP3 WILD-TYPE  255  524
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  FEMALE              3              255
  MALE                2              524
[1] 2 2
[1] FALSE
D45V8, 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                                   282
D45V9, 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              282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      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-B8-5158       TCGA-B8-5164       TCGA-B8-5550 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7       TCGA-2Z-A9J8 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM       TCGA-2Z-A9JN 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-5P-A9KE       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-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-GL-A9DD       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-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-Y8-A8RY 
"RIMBP3 WILD-TYPE" 
D45V11, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               66 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      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-2Z-A9J3 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JN 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       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-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-Y8-A896       TCGA-Y8-A8RY 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMBP3 MUTATED                                  0     0
  RIMBP3 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RIMBP3 MUTATED                           0     5
  RIMBP3 WILD-TYPE                        83   658
D45V12, multiclass
                                  clus
vv                                 RIMBP3 MUTATED RIMBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         5              658
[1] 4 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
  RIMBP3 MUTATED     0   3
  RIMBP3 WILD-TYPE  36 552
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      0    3
  RIMBP3 WILD-TYPE   36  552
                        clus
vv                       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              3              552
[1] 2 2
[1] FALSE

Clustering(46) Variable = FAT1 MUTATION ANALYSIS
D46V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    15   5
  FAT1 WILD-TYPE 563 197
  FAT1 MUTATED FAT1 WILD-TYPE 
            20            760 
  FAT1 MUTATED FAT1 WILD-TYPE 
             5            197 
$`FAT1 MUTATED`
TCGA-B8-4621 TCGA-KN-8436 TCGA-B0-5098 TCGA-B0-5713 TCGA-B8-5550 TCGA-BP-4169 
       25.91        42.35        52.08        91.46        48.53        23.05 
TCGA-CJ-4641 TCGA-CZ-4859 TCGA-4A-A93X TCGA-B9-7268 TCGA-B9-A69E TCGA-BQ-5877 
       54.61        58.75        12.82        22.06        14.86         8.88 
TCGA-BQ-5885 TCGA-G7-6797 TCGA-G7-A8LE TCGA-GL-A9DD TCGA-IZ-8195 TCGA-MH-A562 
       30.28        25.15        80.65        11.21        22.26        20.25 
TCGA-P4-A5E8 TCGA-WN-AB4C 
       42.94        39.06 

$`FAT1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4158 
       70.68       119.38       126.05        24.82         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 
       16.60         6.38         0.53        34.39        14.30        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22        14.17       106.16       114.41        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       69.21        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W8 
       26.40        20.61         0.46         1.15        43.99        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        0.16        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       51.78        90.90        11.05        39.25        71.44        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 
       25.84        25.25        17.98        23.08        16.90       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       88.24        96.69        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       30.38        27.65        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        26.01        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  FAT1 MUTATED FAT1 WILD-TYPE 
          8.88           0.07 
  FAT1 MUTATED FAT1 WILD-TYPE 
         91.46         194.79 
  FAT1 MUTATED FAT1 WILD-TYPE 
        28.095         37.120 
[1] "8.9 - 91.5 (28.1)"  "0.1 - 194.8 (37.1)"
[1] "hr=" "1.1"
D46V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         7        4         6        3
  FAT1 WILD-TYPE     392       85       169       90
D46V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              7            392
  STAGE II             4             85
  STAGE III            6            169
  STAGE IV             3             90
[1] 4 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   5   7   0
  FAT1 WILD-TYPE 415 106 230  11
D46V4, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  T1            8            415
  T2            5            106
  T3            7            230
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FAT1 MUTATED     7   3   0
  FAT1 WILD-TYPE 286  37   5
D46V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0            7            286
  N1            3             37
  N2            0              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"
D46V6, binary
                cls
clus               0   1
  FAT1 MUTATED     9   2
  FAT1 WILD-TYPE 485  79
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      9    2
  FAT1 WILD-TYPE  485   79
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0            9            485
  1            2             79
[1] 2 2
[1] FALSE
D46V7, binary
                cls
clus               0   1
  FAT1 MUTATED     6  14
  FAT1 WILD-TYPE 252 512
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      6   14
  FAT1 WILD-TYPE  252  512
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE            6            252
  MALE             14            512
[1] 2 2
[1] FALSE
D46V8, continuous
                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                                      12
  FAT1 WILD-TYPE                                   270
D46V9, multiclass
                                       clus
vv                                      FAT1 MUTATED FAT1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                7            429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           12            270
[1] 3 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
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  0     0
  FAT1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           4    16
  FAT1 WILD-TYPE                        79   647
D46V12, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   4             79
  WHITE                                      16            647
[1] 4 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
  FAT1 MUTATED     0  17
  FAT1 WILD-TYPE  36 538
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      0   17
  FAT1 WILD-TYPE   36  538
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO           17            538
[1] 2 2
[1] FALSE

Clustering(47) Variable = FAM178A MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  FAM178A MUTATED     2   6
  FAM178A WILD-TYPE 576 196
  FAM178A MUTATED FAM178A WILD-TYPE 
                8               772 
  FAM178A MUTATED FAM178A WILD-TYPE 
                6               196 
$`FAM178A MUTATED`
TCGA-2Z-A9JS TCGA-B0-5098 TCGA-B4-5835 TCGA-BP-4169 TCGA-BP-5173 TCGA-CJ-4920 
       16.18        52.08         0.53        23.05         2.04         4.57 
TCGA-CJ-5677 TCGA-AT-A5NU 
       25.71         2.20 

$`FAM178A WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-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-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  FAM178A MUTATED FAM178A WILD-TYPE 
             0.53              0.07 
  FAM178A MUTATED FAM178A WILD-TYPE 
            52.08            194.79 
  FAM178A MUTATED FAM178A WILD-TYPE 
           10.375            37.250 
[1] "0.5 - 52.1 (10.4)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "8.3"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM178A MUTATED         6        1         0        1
  FAM178A WILD-TYPE     393       88       175       92
D47V3, multiclass
           clus
vv          FAM178A MUTATED FAM178A WILD-TYPE
  STAGE I                 6               393
  STAGE II                1                88
  STAGE III               0               175
  STAGE IV                1                92
[1] 4 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
  FAM178A MUTATED     6   1   1   0
  FAM178A WILD-TYPE 417 110 236  11
D47V4, multiclass
    clus
vv   FAM178A MUTATED FAM178A WILD-TYPE
  T1               6               417
  T2               1               110
  T3               1               236
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM178A MUTATED     2   0   0
  FAM178A WILD-TYPE 291  40   5
D47V5, multiclass
[1] "Remove cluster labels:" "FAM178A MUTATED"       
clus
  FAM178A MUTATED FAM178A WILD-TYPE 
                2               336 
       TCGA-KL-8328        TCGA-KL-8339        TCGA-KN-8430        TCGA-A3-3358 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-AK-3425        TCGA-AK-3450        TCGA-B0-5088        TCGA-B0-5691 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5698        TCGA-B8-4621 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4158        TCGA-BP-4160        TCGA-BP-4331        TCGA-BP-4342 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4795        TCGA-BP-4799        TCGA-BP-4986        TCGA-BP-4988 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4995        TCGA-BP-5006        TCGA-BP-5191        TCGA-BP-5199 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-5201        TCGA-CJ-4636        TCGA-CJ-4891        TCGA-CJ-4894 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-4904        TCGA-CJ-6030        TCGA-CZ-4854        TCGA-CZ-4856 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-5P-A9JU        TCGA-A4-A5Y1        TCGA-B1-A47O        TCGA-B1-A657 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5892        TCGA-BQ-7056        TCGA-IA-A83W 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8329 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332        TCGA-KL-8333 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336        TCGA-KL-8337 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8340        TCGA-KL-8341        TCGA-KL-8342 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345        TCGA-KL-8346 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418        TCGA-KN-8419 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423        TCGA-KN-8424 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428        TCGA-KN-8429 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KO-8405        TCGA-KO-8406        TCGA-KO-8407        TCGA-KO-8408 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8410        TCGA-KO-8413        TCGA-KO-8414 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KO-8415        TCGA-KO-8416        TCGA-KO-8417        TCGA-A3-3313 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A3-3317        TCGA-A3-3331        TCGA-A3-3347        TCGA-A3-3349 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A3-3357        TCGA-A3-3362        TCGA-A3-3367        TCGA-A3-3370 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A3-3373        TCGA-A3-3374        TCGA-A3-3376        TCGA-A3-3385 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A3-3387        TCGA-AK-3427        TCGA-AK-3428        TCGA-AK-3429 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-AK-3430        TCGA-AK-3436        TCGA-AK-3443        TCGA-AK-3451 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-AK-3456        TCGA-B0-4690        TCGA-B0-4691        TCGA-B0-4693 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-4703        TCGA-B0-4710        TCGA-B0-4810        TCGA-B0-4811 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-4814        TCGA-B0-4816        TCGA-B0-4817        TCGA-B0-4823 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4833        TCGA-B0-4837 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-4838        TCGA-B0-4839        TCGA-B0-4842        TCGA-B0-4843 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-4846        TCGA-B0-4852        TCGA-B0-4945        TCGA-B0-5075 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5077        TCGA-B0-5080        TCGA-B0-5081        TCGA-B0-5083 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5092        TCGA-B0-5094 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5095        TCGA-B0-5096        TCGA-B0-5097        TCGA-B0-5104 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5106        TCGA-B0-5107        TCGA-B0-5108        TCGA-B0-5109 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5110        TCGA-B0-5113        TCGA-B0-5115        TCGA-B0-5116 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5119        TCGA-B0-5120        TCGA-B0-5121        TCGA-B0-5399 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5400        TCGA-B0-5692        TCGA-B0-5696        TCGA-B0-5697 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5699        TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5705        TCGA-B0-5706        TCGA-B0-5707        TCGA-B0-5710 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B0-5712        TCGA-B0-5713        TCGA-B2-5633        TCGA-B2-5641 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834        TCGA-B4-5836 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B8-4148        TCGA-B8-4151        TCGA-B8-4154        TCGA-B8-4619 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B8-4620        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4159        TCGA-BP-4162        TCGA-BP-4163 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4165        TCGA-BP-4166        TCGA-BP-4170        TCGA-BP-4173 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4174        TCGA-BP-4326        TCGA-BP-4329        TCGA-BP-4330 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4337        TCGA-BP-4338        TCGA-BP-4340        TCGA-BP-4343 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4345        TCGA-BP-4346        TCGA-BP-4351        TCGA-BP-4352 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4354        TCGA-BP-4756        TCGA-BP-4761        TCGA-BP-4768 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4770        TCGA-BP-4771        TCGA-BP-4787        TCGA-BP-4797 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4798        TCGA-BP-4960        TCGA-BP-4964        TCGA-BP-4967 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4968        TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4974 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-4985        TCGA-BP-4989        TCGA-BP-5007        TCGA-BP-5010 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BP-5169        TCGA-BP-5182        TCGA-BP-5186        TCGA-BP-5198 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-4638        TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4643 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-4644        TCGA-CJ-4868        TCGA-CJ-4869        TCGA-CJ-4872 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-4873        TCGA-CJ-4874        TCGA-CJ-4876        TCGA-CJ-4890 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-4892        TCGA-CJ-4900        TCGA-CJ-4918        TCGA-CJ-5678 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-6033        TCGA-CW-5585        TCGA-CW-5591        TCGA-CW-6087 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-4857        TCGA-CZ-4859        TCGA-CZ-4863        TCGA-CZ-5451 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-5452        TCGA-CZ-5454        TCGA-CZ-5456        TCGA-CZ-5467 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5984        TCGA-CZ-5985 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-5986        TCGA-CZ-5988        TCGA-CZ-5989        TCGA-2Z-A9J1 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93X        TCGA-4A-A93Y 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-A7UZ        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5893 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-BQ-7051        TCGA-DW-7963        TCGA-DZ-6131        TCGA-F9-A8NY 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6789        TCGA-G7-6793        TCGA-G7-6795 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LD        TCGA-GL-6846        TCGA-GL-7966 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-GL-A59R        TCGA-GL-A9DC        TCGA-IA-A40U        TCGA-IA-A40Y 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-J7-A8I2        TCGA-KV-A74V 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-A5E8        TCGA-P4-A5EA        TCGA-P4-AAVL 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A7SM        TCGA-SX-A7SP        TCGA-SX-A7SS 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-UN-AAZ9        TCGA-UZ-A9PM        TCGA-UZ-A9PX        TCGA-Y8-A897 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
D47V6, binary
                   cls
clus                  0   1
  FAM178A MUTATED     5   1
  FAM178A WILD-TYPE 489  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      5    1
  FAM178A WILD-TYPE  489   80
   clus
vv  FAM178A MUTATED FAM178A WILD-TYPE
  0               5               489
  1               1                80
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  FAM178A MUTATED     5   3
  FAM178A WILD-TYPE 253 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      5    3
  FAM178A WILD-TYPE  253  523
        clus
vv       FAM178A MUTATED FAM178A WILD-TYPE
  FEMALE               5               253
  MALE                 3               523
[1] 2 2
[1] FALSE
D47V8, continuous
[1] "Remove cluster labels:" "FAM178A MUTATED"       
clus
  FAM178A MUTATED FAM178A WILD-TYPE 
                1               125 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-5P-A9JU        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CJ-6028        TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-5456 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-CZ-5982        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-EU-5907        TCGA-2Z-A9JE        TCGA-2Z-A9JK        TCGA-2Z-A9JN 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466        TCGA-DW-7963 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A7Q0 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UZ-A9PL 
"FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" "FAM178A WILD-TYPE" 
       TCGA-V9-A7HT 
"FAM178A WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM178A MUTATED                    0                                 6
  FAM178A WILD-TYPE                 66                               430
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM178A MUTATED                                       2
  FAM178A WILD-TYPE                                   280
D47V9, multiclass
                                       clus
vv                                      FAM178A MUTATED FAM178A WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   6               430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               280
[1] 3 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
D47V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM178A MUTATED                                  0     0
  FAM178A WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM178A MUTATED                           1     7
  FAM178A WILD-TYPE                        82   656
D47V12, multiclass
                                  clus
vv                                 FAM178A MUTATED FAM178A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      1                82
  WHITE                                          7               656
[1] 4 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
  FAM178A MUTATED     1   5
  FAM178A WILD-TYPE  35 550
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM178A MUTATED      1    5
  FAM178A WILD-TYPE   35  550
                        clus
vv                       FAM178A MUTATED FAM178A WILD-TYPE
  HISPANIC OR LATINO                   1                35
  NOT HISPANIC OR LATINO               5               550
[1] 2 2
[1] FALSE

Clustering(48) Variable = TCEB1 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  TCEB1 MUTATED     4   0
  TCEB1 WILD-TYPE 574 202
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              4             776 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              0             202 
$`TCEB1 MUTATED`
TCGA-CZ-4862 TCGA-5P-A9JV TCGA-B8-5545 TCGA-CJ-4889 
      107.54        67.17        50.14        63.98 

$`TCEB1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
        0.59         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-7584 
       25.58        16.18        22.49        12.26        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        51.52       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  TCEB1 MUTATED TCEB1 WILD-TYPE 
          50.14            0.07 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
         107.54          194.79 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
         65.575          36.900 
[1] "50.1 - 107.5 (65.6)" "0.1 - 194.8 (36.9)" 
[1] "hr="     "3300000"
D48V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TCEB1 MUTATED         3        0         0        0
  TCEB1 WILD-TYPE     396       89       175       93
D48V3, multiclass
           clus
vv          TCEB1 MUTATED TCEB1 WILD-TYPE
  STAGE I               3             396
  STAGE II              0              89
  STAGE III             0             175
  STAGE IV              0              93
[1] 4 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
  TCEB1 MUTATED     4   0   0   0
  TCEB1 WILD-TYPE 419 111 237  11
D48V4, multiclass
    clus
vv   TCEB1 MUTATED TCEB1 WILD-TYPE
  T1             4             419
  T2             0             111
  T3             0             237
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TCEB1 MUTATED     1   0   0
  TCEB1 WILD-TYPE 292  40   5
D48V5, multiclass
[1] "Remove cluster labels:" "TCEB1 MUTATED"         
clus
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              1             337 
     TCGA-KL-8328      TCGA-KL-8339      TCGA-KN-8430      TCGA-A3-3358 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3450      TCGA-B0-5088      TCGA-B0-5691 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5698      TCGA-B8-4621 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4160      TCGA-BP-4331      TCGA-BP-4342 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4799      TCGA-BP-4986      TCGA-BP-4988 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5191      TCGA-BP-5199 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4891      TCGA-CJ-4894 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-6030      TCGA-CZ-4854      TCGA-CZ-4856 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8329 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418      TCGA-KN-8419 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423      TCGA-KN-8424 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8410      TCGA-KO-8413      TCGA-KO-8414 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8415      TCGA-KO-8416      TCGA-KO-8417      TCGA-A3-3313 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347      TCGA-A3-3349 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3357      TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3373      TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3451 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AK-3456      TCGA-B0-4690      TCGA-B0-4691      TCGA-B0-4693 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4703      TCGA-B0-4710      TCGA-B0-4810      TCGA-B0-4811 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4814      TCGA-B0-4816      TCGA-B0-4817      TCGA-B0-4823 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5092      TCGA-B0-5094 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5119      TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5400      TCGA-B0-5692      TCGA-B0-5696      TCGA-B0-5697 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5699      TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5705      TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5712      TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4622      TCGA-B8-5158 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-5159      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4159      TCGA-BP-4162      TCGA-BP-4163 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4330      TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4960      TCGA-BP-4964 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4989      TCGA-BP-5007 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5198      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4890      TCGA-CJ-4892      TCGA-CJ-4900      TCGA-CJ-4918 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CW-6087      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93X 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466      TCGA-AL-3472 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-F9-A8NY      TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KV-A74V      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-P4-AAVL      TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-Y8-A897 
"TCEB1 WILD-TYPE" 
D48V6, binary
                 cls
clus                0   1
  TCEB1 MUTATED     3   0
  TCEB1 WILD-TYPE 491  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      3    0
  TCEB1 WILD-TYPE  491   81
   clus
vv  TCEB1 MUTATED TCEB1 WILD-TYPE
  0             3             491
  1             0              81
[1] 2 2
[1] FALSE
D48V7, binary
                 cls
clus                0   1
  TCEB1 MUTATED     1   3
  TCEB1 WILD-TYPE 257 523
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      1    3
  TCEB1 WILD-TYPE  257  523
        clus
vv       TCEB1 MUTATED TCEB1 WILD-TYPE
  FEMALE             1             257
  MALE               3             523
[1] 2 2
[1] FALSE
D48V8, continuous
[1] "Remove cluster labels:" "TCEB1 MUTATED"         
clus
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-DV-5565      TCGA-DV-5566 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-V9-A7HT 
"TCEB1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TCEB1 MUTATED                    0                                 3
  TCEB1 WILD-TYPE                 66                               433
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TCEB1 MUTATED                                       1
  TCEB1 WILD-TYPE                                   281
D48V9, multiclass
                                       clus
vv                                      TCEB1 MUTATED TCEB1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             281
[1] 3 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
D48V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEB1 MUTATED                                  0     0
  TCEB1 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TCEB1 MUTATED                           1     3
  TCEB1 WILD-TYPE                        82   660
D48V12, multiclass
                                  clus
vv                                 TCEB1 MUTATED TCEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                        3             660
[1] 4 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
  TCEB1 MUTATED     1   3
  TCEB1 WILD-TYPE  35 552
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      1    3
  TCEB1 WILD-TYPE   35  552
                        clus
vv                       TCEB1 MUTATED TCEB1 WILD-TYPE
  HISPANIC OR LATINO                 1              35
  NOT HISPANIC OR LATINO             3             552
[1] 2 2
[1] FALSE

Clustering(49) Variable = PODXL MUTATION ANALYSIS
D49V1, survival
                 sevent
clus2               0   1
  PODXL MUTATED     6   0
  PODXL WILD-TYPE 572 202
  PODXL MUTATED PODXL WILD-TYPE 
              6             774 
  PODXL MUTATED PODXL WILD-TYPE 
              0             202 
$`PODXL MUTATED`
TCGA-CW-6093 TCGA-CZ-4856 TCGA-KL-8345 TCGA-A3-3317 TCGA-F9-A97G TCGA-Y8-A896 
      103.43         0.59        54.74        49.02         0.43        18.64 

$`PODXL WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4862 
       27.65       108.56       118.85        75.58        46.16       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3322 
       96.62        90.48        92.55        39.16        24.16        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       51.25        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98        42.41       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      123.09       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        31.96        21.30        31.66 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.05        25.28         6.02        13.28 

  PODXL MUTATED PODXL WILD-TYPE 
           0.43            0.07 
  PODXL MUTATED PODXL WILD-TYPE 
         103.43          194.79 
  PODXL MUTATED PODXL WILD-TYPE 
         33.830          36.985 
[1] "0.4 - 103.4 (33.8)" "0.1 - 194.8 (37.0)"
[1] "hr="     "3300000"
D49V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PODXL MUTATED         2        1         3        0
  PODXL WILD-TYPE     397       88       172       93
D49V3, multiclass
           clus
vv          PODXL MUTATED PODXL WILD-TYPE
  STAGE I               2             397
  STAGE II              1              88
  STAGE III             3             172
  STAGE IV              0              93
[1] 4 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
  PODXL MUTATED     2   1   3   0
  PODXL WILD-TYPE 421 110 234  11
D49V4, multiclass
    clus
vv   PODXL MUTATED PODXL WILD-TYPE
  T1             2             421
  T2             1             110
  T3             3             234
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PODXL MUTATED     4   0   0
  PODXL WILD-TYPE 289  40   5
D49V5, multiclass
    clus
vv   PODXL MUTATED PODXL WILD-TYPE
  N0             4             289
  N1             0              40
  N2             0               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"
D49V6, binary
                 cls
clus                0   1
  PODXL MUTATED     5   0
  PODXL WILD-TYPE 489  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      5    0
  PODXL WILD-TYPE  489   81
   clus
vv  PODXL MUTATED PODXL WILD-TYPE
  0             5             489
  1             0              81
[1] 2 2
[1] FALSE
D49V7, binary
                 cls
clus                0   1
  PODXL MUTATED     1   5
  PODXL WILD-TYPE 257 521
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      1    5
  PODXL WILD-TYPE  257  521
        clus
vv       PODXL MUTATED PODXL WILD-TYPE
  FEMALE             1             257
  MALE               5             521
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "PODXL MUTATED"         
clus
  PODXL MUTATED PODXL WILD-TYPE 
              1             125 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4862      TCGA-DV-5565      TCGA-DV-5566 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-CJ-6028      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-CZ-5982      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-EU-5907      TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-G7-7502      TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-SX-A7SM      TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL 
"PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" "PODXL WILD-TYPE" 
     TCGA-V9-A7HT 
"PODXL WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PODXL MUTATED                    1                                 3
  PODXL WILD-TYPE                 65                               433
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PODXL MUTATED                                       2
  PODXL WILD-TYPE                                   280
D49V9, multiclass
                                       clus
vv                                      PODXL MUTATED PODXL WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             280
[1] 3 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
  PODXL MUTATED                                  0     1
  PODXL WILD-TYPE                                2    13
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PODXL MUTATED                           0     4
  PODXL WILD-TYPE                        83   659
D49V12, multiclass
                                  clus
vv                                 PODXL MUTATED PODXL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              13
  BLACK OR AFRICAN AMERICAN                    0              83
  WHITE                                        4             659
[1] 4 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
  PODXL MUTATED     0   4
  PODXL WILD-TYPE  36 551
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PODXL MUTATED      0    4
  PODXL WILD-TYPE   36  551
                        clus
vv                       PODXL MUTATED PODXL WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             4             551
[1] 2 2
[1] FALSE

Clustering(50) Variable = DNAJA3 MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  DNAJA3 MUTATED     3   0
  DNAJA3 WILD-TYPE 575 202
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               3              777 
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               0              202 
$`DNAJA3 MUTATED`
TCGA-A3-3317 TCGA-2Z-A9JN TCGA-SX-A71S 
       49.02        24.33        49.45 

$`DNAJA3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        24.16        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
        6.61        99.12        92.58        16.01        50.60        14.07 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
           24.33             0.07 
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
           49.45           194.79 
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
           49.02            36.95 
[1] "24.3 - 49.5 (49.0)" "0.1 - 194.8 (37.0)"
[1] "hr="     "1200000"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  DNAJA3 MUTATED         2        1         0        0
  DNAJA3 WILD-TYPE     397       88       175       93
D50V3, multiclass
           clus
vv          DNAJA3 MUTATED DNAJA3 WILD-TYPE
  STAGE I                2              397
  STAGE II               1               88
  STAGE III              0              175
  STAGE IV               0               93
[1] 4 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
  DNAJA3 MUTATED     2   1   0   0
  DNAJA3 WILD-TYPE 421 110 237  11
D50V4, multiclass
    clus
vv   DNAJA3 MUTATED DNAJA3 WILD-TYPE
  T1              2              421
  T2              1              110
  T3              0              237
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNAJA3 MUTATED     1   0   0
  DNAJA3 WILD-TYPE 292  40   5
D50V5, multiclass
[1] "Remove cluster labels:" "DNAJA3 MUTATED"        
clus
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               1              337 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4904       TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429       TCGA-AK-3430 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3451       TCGA-AK-3456 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5699 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4162       TCGA-BP-4163 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4960       TCGA-BP-4964 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4989       TCGA-BP-5007 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5198       TCGA-CJ-4638       TCGA-CJ-4639       TCGA-CJ-4640 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874       TCGA-CJ-4876 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4890       TCGA-CJ-4892       TCGA-CJ-4900       TCGA-CJ-4918 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6033       TCGA-CW-5585       TCGA-CW-5591 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CW-6087       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Y8-A897 
"DNAJA3 WILD-TYPE" 
D50V6, binary
                  cls
clus                 0   1
  DNAJA3 MUTATED     2   0
  DNAJA3 WILD-TYPE 492  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA3 MUTATED      2    0
  DNAJA3 WILD-TYPE  492   81
   clus
vv  DNAJA3 MUTATED DNAJA3 WILD-TYPE
  0              2              492
  1              0               81
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  DNAJA3 MUTATED     2   1
  DNAJA3 WILD-TYPE 256 525
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA3 MUTATED      2    1
  DNAJA3 WILD-TYPE  256  525
        clus
vv       DNAJA3 MUTATED DNAJA3 WILD-TYPE
  FEMALE              2              256
  MALE                1              525
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "DNAJA3 MUTATED"        
clus
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-EU-5906       TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL       TCGA-SX-A7SM 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  DNAJA3 MUTATED                    0                                 1
  DNAJA3 WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DNAJA3 MUTATED                                       2
  DNAJA3 WILD-TYPE                                   280
D50V9, multiclass
                                       clus
vv                                      DNAJA3 MUTATED DNAJA3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              280
[1] 3 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:" "DNAJA3 MUTATED"        
clus
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               2               92 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SR 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS       TCGA-UZ-A9PX 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896       TCGA-Y8-A8RY 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
D50V11, continuous
[1] "Remove cluster labels:" "DNAJA3 MUTATED"        
clus
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               2               65 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9J3       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-A4-A48D 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM       TCGA-SX-A7SR 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS       TCGA-UZ-A9PX 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894       TCGA-Y8-A896 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Y8-A8RY 
"DNAJA3 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNAJA3 MUTATED                                  0     0
  DNAJA3 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNAJA3 MUTATED                           1     1
  DNAJA3 WILD-TYPE                        82   662
D50V12, multiclass
[1] "Remove cluster labels:" "DNAJA3 MUTATED"        
clus
  DNAJA3 MUTATED DNAJA3 WILD-TYPE 
               2              760 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KM-8439       TCGA-KM-8441 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8430       TCGA-KO-8411       TCGA-A3-3358       TCGA-AK-3425 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3450       TCGA-AK-3454       TCGA-AK-3455       TCGA-B0-4707 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4712       TCGA-B0-4815       TCGA-B0-5088       TCGA-B0-5691 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5693       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5812       TCGA-B2-5635       TCGA-B8-4621       TCGA-B8-5162 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4164       TCGA-BP-4331 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4342       TCGA-BP-4760       TCGA-BP-4762       TCGA-BP-4775 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4782       TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4807 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4965       TCGA-BP-4976       TCGA-BP-4986       TCGA-BP-4988 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4993       TCGA-BP-4995       TCGA-BP-4999       TCGA-BP-5006 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5009       TCGA-BP-5168       TCGA-BP-5178       TCGA-BP-5181 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5189       TCGA-BP-5191       TCGA-BP-5199       TCGA-BP-5201 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894       TCGA-CJ-4904 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-6027       TCGA-CJ-6030       TCGA-CW-6093       TCGA-CZ-4854 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4862       TCGA-CZ-4865       TCGA-DV-5565 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JD       TCGA-2Z-A9JJ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9JL       TCGA-2Z-A9JQ       TCGA-2Z-A9JS       TCGA-2Z-A9JT 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-5P-A9JV       TCGA-A4-7288       TCGA-A4-7584 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-7734       TCGA-A4-A5Y1       TCGA-AL-3468       TCGA-AL-A5DJ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B1-A47M       TCGA-B1-A47O       TCGA-B1-A657       TCGA-B3-A6W5 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-5155       TCGA-B9-A44B       TCGA-B9-A5W7       TCGA-BQ-5886 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7046       TCGA-BQ-7049 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-7055       TCGA-BQ-7056       TCGA-BQ-7058       TCGA-DW-5560 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836       TCGA-DW-7837 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DZ-6134       TCGA-GL-A59T       TCGA-IA-A83W 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-MH-A855       TCGA-MH-A857       TCGA-PJ-A5Z8 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-PJ-A5Z9       TCGA-PJ-A8JU       TCGA-SX-A71W       TCGA-SX-A7SO 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-UZ-A9PZ       TCGA-Y8-A895 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Y8-A898       TCGA-Y8-A8RZ       TCGA-KL-8323       TCGA-KL-8324 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8325       TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8440       TCGA-KM-8443       TCGA-KM-8476 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KM-8477       TCGA-KM-8639       TCGA-KN-8418       TCGA-KN-8419 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8426       TCGA-KN-8427       TCGA-KN-8428 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8432       TCGA-KN-8433       TCGA-KN-8434 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KN-8435       TCGA-KN-8436       TCGA-KN-8437       TCGA-KO-8403 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8404       TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3313       TCGA-A3-3322       TCGA-A3-3323       TCGA-A3-3326 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349       TCGA-A3-3357 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385       TCGA-A3-3387 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429       TCGA-AK-3430 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3431       TCGA-AK-3434       TCGA-AK-3436       TCGA-AK-3440 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3443       TCGA-AK-3445       TCGA-AK-3451       TCGA-AK-3453 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3456       TCGA-AK-3458       TCGA-AK-3460       TCGA-AK-3461 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AK-3465       TCGA-AS-3777       TCGA-B0-4690       TCGA-B0-4691 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4694       TCGA-B0-4697       TCGA-B0-4700 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4706       TCGA-B0-4710       TCGA-B0-4713 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4714       TCGA-B0-4718       TCGA-B0-4810       TCGA-B0-4811 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4813       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4818       TCGA-B0-4819       TCGA-B0-4822       TCGA-B0-4823 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4828       TCGA-B0-4833 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4836       TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4841       TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4844 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4845       TCGA-B0-4846       TCGA-B0-4847       TCGA-B0-4848 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-4849       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5098 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5099       TCGA-B0-5100       TCGA-B0-5102       TCGA-B0-5104 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5117       TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5402       TCGA-B0-5692 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5699       TCGA-B0-5701 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5709       TCGA-B0-5710       TCGA-B0-5711 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-3923       TCGA-B2-3924 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B2-4098       TCGA-B2-4099       TCGA-B2-4101       TCGA-B2-5633 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4146       TCGA-B8-4148 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4153       TCGA-B8-4154       TCGA-B8-4619 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B8-5552       TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4161 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4167       TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4174       TCGA-BP-4176       TCGA-BP-4177       TCGA-BP-4326 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4340       TCGA-BP-4341       TCGA-BP-4343       TCGA-BP-4345 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4346       TCGA-BP-4347       TCGA-BP-4349       TCGA-BP-4351 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4355       TCGA-BP-4756 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4758       TCGA-BP-4759       TCGA-BP-4761       TCGA-BP-4763 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4765       TCGA-BP-4766       TCGA-BP-4768       TCGA-BP-4770 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4771       TCGA-BP-4774       TCGA-BP-4777       TCGA-BP-4781 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4787       TCGA-BP-4789       TCGA-BP-4790       TCGA-BP-4797 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4798       TCGA-BP-4801       TCGA-BP-4803       TCGA-BP-4804 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4961       TCGA-BP-4962       TCGA-BP-4963 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4972       TCGA-BP-4973       TCGA-BP-4974 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4975       TCGA-BP-4977       TCGA-BP-4981       TCGA-BP-4982 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4983       TCGA-BP-4985       TCGA-BP-4987       TCGA-BP-4989 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-4991       TCGA-BP-4992       TCGA-BP-4994       TCGA-BP-4998 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5000       TCGA-BP-5001       TCGA-BP-5004       TCGA-BP-5007 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5008       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5170 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5173       TCGA-BP-5174       TCGA-BP-5175       TCGA-BP-5176 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5177       TCGA-BP-5180       TCGA-BP-5182       TCGA-BP-5183 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5184       TCGA-BP-5185       TCGA-BP-5186       TCGA-BP-5187 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5190       TCGA-BP-5192       TCGA-BP-5194       TCGA-BP-5195 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BP-5196       TCGA-BP-5198       TCGA-BP-5200       TCGA-BP-5202 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4634       TCGA-CJ-4635       TCGA-CJ-4637       TCGA-CJ-4638 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4641       TCGA-CJ-4643 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4870 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4871       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4875       TCGA-CJ-4876       TCGA-CJ-4878       TCGA-CJ-4881 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4882       TCGA-CJ-4884       TCGA-CJ-4885       TCGA-CJ-4886 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4887       TCGA-CJ-4888       TCGA-CJ-4889       TCGA-CJ-4890 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4893       TCGA-CJ-4895       TCGA-CJ-4897 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4899       TCGA-CJ-4900       TCGA-CJ-4901       TCGA-CJ-4902 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4903       TCGA-CJ-4905       TCGA-CJ-4907       TCGA-CJ-4908 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4912       TCGA-CJ-4913       TCGA-CJ-4916       TCGA-CJ-4918 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-4920       TCGA-CJ-4923       TCGA-CJ-5671       TCGA-CJ-5672 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-5675       TCGA-CJ-5676       TCGA-CJ-5677       TCGA-CJ-5678 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-5679       TCGA-CJ-5680       TCGA-CJ-5681       TCGA-CJ-5682 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-5683       TCGA-CJ-5684       TCGA-CJ-5686       TCGA-CJ-6028 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CJ-6031       TCGA-CJ-6032       TCGA-CJ-6033       TCGA-CW-5580 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CW-5581       TCGA-CW-5583       TCGA-CW-5585       TCGA-CW-5588 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CW-5589       TCGA-CW-5591       TCGA-CW-6087       TCGA-CW-6090 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CW-6097       TCGA-CZ-4853       TCGA-CZ-4857       TCGA-CZ-4858 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-4859       TCGA-CZ-4861       TCGA-CZ-4863       TCGA-CZ-4866 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5453       TCGA-CZ-5454 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5455       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5459       TCGA-CZ-5460       TCGA-CZ-5461       TCGA-CZ-5462 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5463       TCGA-CZ-5467       TCGA-CZ-5468       TCGA-CZ-5469 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-CZ-5984       TCGA-CZ-5985       TCGA-CZ-5986 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-CZ-5987       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-EU-5904 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-EU-5905       TCGA-EU-5906       TCGA-EU-5907       TCGA-2K-A9WE 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9J2       TCGA-2Z-A9J3       TCGA-2Z-A9J5 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9J6       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JE 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9JG       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-2Z-A9JP       TCGA-2Z-A9JR       TCGA-4A-A93W 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-5P-A9JW       TCGA-5P-A9JY 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9JZ       TCGA-5P-A9K0       TCGA-5P-A9K2       TCGA-5P-A9K3 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9K6       TCGA-5P-A9K8       TCGA-5P-A9KA       TCGA-5P-A9KC 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-5P-A9KH       TCGA-A4-7286       TCGA-A4-7287 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7732       TCGA-A4-7828 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-7915       TCGA-A4-7996       TCGA-A4-7997       TCGA-A4-8098 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-8310       TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8515 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A48D 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-A4-A6HP       TCGA-A4-A772       TCGA-A4-A7UZ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3467       TCGA-AL-3472       TCGA-AL-3473 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-AL-7173       TCGA-AT-A5NU       TCGA-B1-5398       TCGA-B1-7332 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B1-A47N       TCGA-B1-A654       TCGA-B1-A655       TCGA-B1-A656 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B3-3925       TCGA-B3-3926       TCGA-B3-4103       TCGA-B3-4104 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B3-8121       TCGA-B9-4113       TCGA-B9-4114       TCGA-B9-4115 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-4116       TCGA-B9-4117       TCGA-B9-4617       TCGA-B9-5156 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A5W8       TCGA-B9-A5W9       TCGA-B9-A69E 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-B9-A8YH       TCGA-B9-A8YI       TCGA-BQ-5875       TCGA-BQ-5876 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879       TCGA-BQ-5880 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5881       TCGA-BQ-5883       TCGA-BQ-5884       TCGA-BQ-5885 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-7044       TCGA-BQ-7045       TCGA-BQ-7048 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7053       TCGA-BQ-7059 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-BQ-7060       TCGA-BQ-7061       TCGA-BQ-7062       TCGA-DW-7963 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-DZ-6131       TCGA-DZ-6133       TCGA-EV-5901       TCGA-EV-5902 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-EV-5903       TCGA-F9-A4JJ       TCGA-F9-A7Q0       TCGA-F9-A7VF 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6790 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-6796 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LC       TCGA-G7-A8LD       TCGA-G7-A8LE 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-6846       TCGA-GL-7773       TCGA-GL-7966       TCGA-GL-8500 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-A4EM       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-GL-A9DD 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-GL-A9DE       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IA-A83S       TCGA-IA-A83T       TCGA-IA-A83V       TCGA-IZ-8195 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-IZ-8196       TCGA-IZ-A6M9       TCGA-J7-6720       TCGA-J7-8537 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-J7-A8I2       TCGA-KV-A6GD       TCGA-KV-A6GE       TCGA-KV-A74V 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-MH-A55W       TCGA-MH-A55Z       TCGA-MH-A560       TCGA-MH-A561 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-MH-A562       TCGA-MH-A854       TCGA-MH-A856       TCGA-O9-A75Z 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-P4-A5E6       TCGA-P4-A5E7       TCGA-P4-A5E8       TCGA-P4-A5EA 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-P4-A5EB       TCGA-P4-A5ED       TCGA-P4-AAVL       TCGA-P4-AAVM 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71R       TCGA-SX-A71U       TCGA-SX-A71V 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PJ 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-UZ-A9PK       TCGA-UZ-A9PL       TCGA-UZ-A9PM       TCGA-UZ-A9PN 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-UZ-A9PP       TCGA-UZ-A9PS       TCGA-UZ-A9PU       TCGA-UZ-A9PV 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-UZ-A9Q0       TCGA-UZ-A9Q1       TCGA-V9-A7HT 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894       TCGA-Y8-A896 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
      TCGA-Y8-A897       TCGA-Y8-A8RY       TCGA-Y8-A8S0       TCGA-Y8-A8S1 
"DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" "DNAJA3 WILD-TYPE" 
D50V13, binary
                  cls
clus                 0   1
  DNAJA3 MUTATED     0   2
  DNAJA3 WILD-TYPE  36 553
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNAJA3 MUTATED      0    2
  DNAJA3 WILD-TYPE   36  553
                        clus
vv                       DNAJA3 MUTATED DNAJA3 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              2              553
[1] 2 2
[1] FALSE

Clustering(51) Variable = NASP MUTATION ANALYSIS
D51V1, survival
                sevent
clus2              0   1
  NASP MUTATED     3   2
  NASP WILD-TYPE 575 200
  NASP MUTATED NASP WILD-TYPE 
             5            775 
  NASP MUTATED NASP WILD-TYPE 
             2            200 
$`NASP MUTATED`
TCGA-KN-8433 TCGA-KO-8415 TCGA-CJ-5679 TCGA-2Z-A9JE TCGA-P4-A5EA 
       11.21        96.62        22.32        56.81         6.61 

$`NASP WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3313 
       99.88       105.60        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JG 
       58.22       100.27        56.91         4.57        91.73        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  NASP MUTATED NASP WILD-TYPE 
          6.61           0.07 
  NASP MUTATED NASP WILD-TYPE 
         96.62         194.79 
  NASP MUTATED NASP WILD-TYPE 
         22.32          37.02 
[1] "6.6 - 96.6 (22.3)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "1.7"
D51V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NASP MUTATED         2        0         3        0
  NASP WILD-TYPE     397       89       172       93
D51V3, multiclass
           clus
vv          NASP MUTATED NASP WILD-TYPE
  STAGE I              2            397
  STAGE II             0             89
  STAGE III            3            172
  STAGE IV             0             93
[1] 4 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     2   0   3   0
  NASP WILD-TYPE 421 111 234  11
D51V4, multiclass
    clus
vv   NASP MUTATED NASP WILD-TYPE
  T1            2            421
  T2            0            111
  T3            3            234
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NASP MUTATED     1   1   0
  NASP WILD-TYPE 292  39   5
D51V5, multiclass
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             2            336 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-KL-8326     TCGA-KL-8327     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-8340     TCGA-KL-8341     TCGA-KL-8342 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8405     TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313     TCGA-A3-3317 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3357 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385     TCGA-A3-3387 
"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-3451     TCGA-AK-3456 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693     TCGA-B0-4703 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4814 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823     TCGA-B0-4824 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837     TCGA-B0-4838 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843     TCGA-B0-4846 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075     TCGA-B0-5077 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083     TCGA-B0-5084 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5085     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5699 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4330     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5198     TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4890     TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-F9-A8NY     TCGA-F9-A97G     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-G7-A8LD     TCGA-GL-6846 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-AAVL 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP     TCGA-SX-A7SS 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX     TCGA-Y8-A897 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
D51V6, binary
                cls
clus               0   1
  NASP MUTATED     2   0
  NASP WILD-TYPE 492  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      2    0
  NASP WILD-TYPE  492   81
   clus
vv  NASP MUTATED NASP WILD-TYPE
  0            2            492
  1            0             81
[1] 2 2
[1] FALSE
D51V7, binary
                cls
clus               0   1
  NASP MUTATED     3   2
  NASP WILD-TYPE 255 524
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      3    2
  NASP WILD-TYPE  255  524
        clus
vv       NASP MUTATED NASP WILD-TYPE
  FEMALE            3            255
  MALE              2            524
[1] 2 2
[1] FALSE
D51V8, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1            125 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-7836     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4622 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-EU-5904     TCGA-EU-5905 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-EU-5906     TCGA-EU-5907     TCGA-2Z-A9JK     TCGA-2Z-A9JN 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-7963 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A7Q0 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SP     TCGA-SX-A7SQ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-V9-A7HT 
"NASP WILD-TYPE" 
                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                                       2
  NASP WILD-TYPE                                   280
D51V9, multiclass
                                       clus
vv                                      NASP MUTATED NASP WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            280
[1] 3 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
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    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-B8-5158     TCGA-B8-5164     TCGA-B8-5550 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7     TCGA-2Z-A9J8 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM     TCGA-2Z-A9JN 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     TCGA-5P-A9K3 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-5P-A9KE     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-A69E     TCGA-DW-7963     TCGA-F9-A97G 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-GL-7773 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-A9DD     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-IA-A83S     TCGA-IA-A83V     TCGA-MH-A854 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-Q2-A5QZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-Y8-A8RY 
"NASP WILD-TYPE" 
D51V11, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             66 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    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-2Z-A9J3 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JN 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y     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-7963     TCGA-F9-A97G     TCGA-G7-6793     TCGA-G7-6795 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-IA-A40U 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6     TCGA-Q2-A5QZ 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"NASP WILD-TYPE" "NASP WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NASP MUTATED                                  0     0
  NASP WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NASP MUTATED                           0     5
  NASP WILD-TYPE                        83   658
D51V12, multiclass
                                  clus
vv                                 NASP MUTATED NASP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                       5            658
[1] 4 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
  NASP MUTATED     1   4
  NASP WILD-TYPE  35 551
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      1    4
  NASP WILD-TYPE   35  551
                        clus
vv                       NASP MUTATED NASP WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO            4            551
[1] 2 2
[1] FALSE

Clustering(52) Variable = SLC23A1 MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  SLC23A1 MUTATED     6   0
  SLC23A1 WILD-TYPE 572 202
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                6               774 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                0               202 
$`SLC23A1 MUTATED`
TCGA-A3-3322 TCGA-A3-3370 TCGA-B0-5712 TCGA-CJ-4634 TCGA-MH-A55Z TCGA-SX-A7SS 
       48.59        74.76        89.49       115.00        27.78        53.10 

$`SLC23A1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        24.16        49.02        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3373 
       52.93        45.53        88.37        51.25        74.63        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
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-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
            27.78              0.07 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
           115.00            194.79 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
            63.93             36.90 
[1] "27.8 - 115.0 (63.9)" "0.1 - 194.8 (36.9)" 
[1] "hr="     "9100000"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC23A1 MUTATED         5        0         0        1
  SLC23A1 WILD-TYPE     394       89       175       92
D52V3, multiclass
           clus
vv          SLC23A1 MUTATED SLC23A1 WILD-TYPE
  STAGE I                 5               394
  STAGE II                0                89
  STAGE III               0               175
  STAGE IV                1                92
[1] 4 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
  SLC23A1 MUTATED     5   1   0   0
  SLC23A1 WILD-TYPE 418 110 237  11
D52V4, multiclass
    clus
vv   SLC23A1 MUTATED SLC23A1 WILD-TYPE
  T1               5               418
  T2               1               110
  T3               0               237
  T4               0                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC23A1 MUTATED     3   0   0
  SLC23A1 WILD-TYPE 290  40   5
D52V5, multiclass
    clus
vv   SLC23A1 MUTATED SLC23A1 WILD-TYPE
  N0               3               290
  N1               0                40
  N2               0                 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
  SLC23A1 MUTATED     4   1
  SLC23A1 WILD-TYPE 490  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      4    1
  SLC23A1 WILD-TYPE  490   80
   clus
vv  SLC23A1 MUTATED SLC23A1 WILD-TYPE
  0               4               490
  1               1                80
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  SLC23A1 MUTATED     3   3
  SLC23A1 WILD-TYPE 255 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      3    3
  SLC23A1 WILD-TYPE  255  523
        clus
vv       SLC23A1 MUTATED SLC23A1 WILD-TYPE
  FEMALE               3               255
  MALE                 3               523
[1] 2 2
[1] FALSE
D52V8, continuous
[1] "Remove cluster labels:" "SLC23A1 MUTATED"       
clus
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                1               125 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-5P-A9JU        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A7SO        TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-AK-3430        TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4622 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B8-5158        TCGA-CJ-6028        TCGA-CZ-4858        TCGA-CZ-4861 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5458        TCGA-CZ-5465 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-EU-5904        TCGA-EU-5905 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-EU-5906        TCGA-EU-5907        TCGA-2Z-A9JE        TCGA-2Z-A9JK 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-4A-A93W        TCGA-4A-A93X        TCGA-4A-A93Y 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8098        TCGA-A4-8310 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8517        TCGA-A4-8518 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-8630        TCGA-A4-A48D        TCGA-A4-A4ZT        TCGA-A4-A57E 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP        TCGA-AL-3466 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-DW-7963        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-F9-A7Q0        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-G7-A4TM        TCGA-G7-A8LB 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-A8LC        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-IA-A40U 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-IA-A40X        TCGA-IA-A40Y        TCGA-J7-8537        TCGA-Q2-A5QZ 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A71R        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A71V 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SN        TCGA-SX-A7SP 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A7SQ        TCGA-SX-A7SR        TCGA-SX-A7SU        TCGA-UZ-A9PL 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-V9-A7HT 
"SLC23A1 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC23A1 MUTATED                    0                                 4
  SLC23A1 WILD-TYPE                 66                               432
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC23A1 MUTATED                                       2
  SLC23A1 WILD-TYPE                                   280
D52V9, multiclass
                                       clus
vv                                      SLC23A1 MUTATED SLC23A1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   4               432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               280
[1] 3 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
[1] "Remove cluster labels:" "SLC23A1 MUTATED"       
clus
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                1                93 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-5P-A9JU 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B9-A44B        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-GL-A59T        TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-AK-3451        TCGA-B8-4146        TCGA-B8-5158        TCGA-B8-5164 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B8-5550        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-5P-A9K3        TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-HE-A5NK        TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-Y8-A8RY 
"SLC23A1 WILD-TYPE" 
D52V11, continuous
[1] "Remove cluster labels:" "SLC23A1 MUTATED"       
clus
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                1                66 
       TCGA-2Z-A9JD        TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-PJ-A8JU 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A71W        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-AK-3445        TCGA-AK-3451        TCGA-B8-5158        TCGA-B8-5550 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6793 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
       TCGA-Y8-A896        TCGA-Y8-A8RY 
"SLC23A1 WILD-TYPE" "SLC23A1 WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC23A1 MUTATED                                  0     0
  SLC23A1 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC23A1 MUTATED                           2     4
  SLC23A1 WILD-TYPE                        81   659
D52V12, multiclass
                                  clus
vv                                 SLC23A1 MUTATED SLC23A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      2                81
  WHITE                                          4               659
[1] 4 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
  SLC23A1 MUTATED     0   5
  SLC23A1 WILD-TYPE  36 550
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      0    5
  SLC23A1 WILD-TYPE   36  550
                        clus
vv                       SLC23A1 MUTATED SLC23A1 WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO               5               550
[1] 2 2
[1] FALSE

Clustering(53) Variable = RILPL1 MUTATION ANALYSIS
D53V1, survival
                  sevent
clus2                0   1
  RILPL1 MUTATED     4   1
  RILPL1 WILD-TYPE 574 201
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               5              775 
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               1              201 
$`RILPL1 MUTATED`
TCGA-KO-8411 TCGA-KL-8333 TCGA-B8-5549 TCGA-SX-A7SM TCGA-UZ-A9PS 
      130.13        98.33         6.38        11.93        71.24 

$`RILPL1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-A3-3358 
      102.81        28.11        23.28        28.80        47.24        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         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-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PU 
      117.40       103.63       125.29        37.35        98.96        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  RILPL1 MUTATED RILPL1 WILD-TYPE 
            6.38             0.07 
  RILPL1 MUTATED RILPL1 WILD-TYPE 
          130.13           194.79 
  RILPL1 MUTATED RILPL1 WILD-TYPE 
           71.24            36.95 
[1] "6.4 - 130.1 (71.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.7"
D53V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RILPL1 MUTATED         2        2         0        1
  RILPL1 WILD-TYPE     397       87       175       92
D53V3, multiclass
           clus
vv          RILPL1 MUTATED RILPL1 WILD-TYPE
  STAGE I                2              397
  STAGE II               2               87
  STAGE III              0              175
  STAGE IV               1               92
[1] 4 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
  RILPL1 MUTATED     2   2   1   0
  RILPL1 WILD-TYPE 421 109 236  11
D53V4, multiclass
    clus
vv   RILPL1 MUTATED RILPL1 WILD-TYPE
  T1              2              421
  T2              2              109
  T3              1              236
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RILPL1 MUTATED     2   1   0
  RILPL1 WILD-TYPE 291  39   5
D53V5, multiclass
    clus
vv   RILPL1 MUTATED RILPL1 WILD-TYPE
  N0              2              291
  N1              1               39
  N2              0                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"
D53V6, binary
                  cls
clus                 0   1
  RILPL1 MUTATED     3   1
  RILPL1 WILD-TYPE 491  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RILPL1 MUTATED      3    1
  RILPL1 WILD-TYPE  491   80
   clus
vv  RILPL1 MUTATED RILPL1 WILD-TYPE
  0              3              491
  1              1               80
[1] 2 2
[1] FALSE
D53V7, binary
                  cls
clus                 0   1
  RILPL1 MUTATED     1   4
  RILPL1 WILD-TYPE 257 522
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RILPL1 MUTATED      1    4
  RILPL1 WILD-TYPE  257  522
        clus
vv       RILPL1 MUTATED RILPL1 WILD-TYPE
  FEMALE              1              257
  MALE                4              522
[1] 2 2
[1] FALSE
D53V8, continuous
[1] "Remove cluster labels:" "RILPL1 MUTATED"        
clus
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               2              124 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-CZ-4854 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565       TCGA-DV-5566 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT       TCGA-5P-A9JU 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7836 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W       TCGA-SX-A7SO 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440       TCGA-KM-8443 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639       TCGA-KN-8429 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428       TCGA-AK-3430 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622       TCGA-B8-5158 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861       TCGA-CZ-5456 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ       TCGA-SX-A7SR 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL       TCGA-V9-A7HT 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RILPL1 MUTATED                    2                                 1
  RILPL1 WILD-TYPE                 64                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RILPL1 MUTATED                                       2
  RILPL1 WILD-TYPE                                   280
D53V9, multiclass
                                       clus
vv                                      RILPL1 MUTATED RILPL1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              280
[1] 3 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:" "RILPL1 MUTATED"        
clus
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               2               92 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-5P-A9K3       TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B9-4117       TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-F9-A97G       TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896       TCGA-Y8-A8RY 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
D53V11, continuous
[1] "Remove cluster labels:" "RILPL1 MUTATED"        
clus
  RILPL1 MUTATED RILPL1 WILD-TYPE 
               2               65 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-2Z-A9J3       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-G7-A8LE       TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-Q2-A5QZ       TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894       TCGA-Y8-A896 
"RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" "RILPL1 WILD-TYPE" 
      TCGA-Y8-A8RY 
"RILPL1 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RILPL1 MUTATED                                  0     0
  RILPL1 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RILPL1 MUTATED                           2     3
  RILPL1 WILD-TYPE                        81   660
D53V12, multiclass
                                  clus
vv                                 RILPL1 MUTATED RILPL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     2               81
  WHITE                                         3              660
[1] 4 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
  RILPL1 MUTATED     0   4
  RILPL1 WILD-TYPE  36 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RILPL1 MUTATED      0    4
  RILPL1 WILD-TYPE   36  551
                        clus
vv                       RILPL1 MUTATED RILPL1 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(54) Variable = NIPBL MUTATION ANALYSIS
D54V1, survival
                 sevent
clus2               0   1
  NIPBL MUTATED    10   5
  NIPBL WILD-TYPE 568 197
  NIPBL MUTATED NIPBL WILD-TYPE 
             15             765 
  NIPBL MUTATED NIPBL WILD-TYPE 
              5             197 
$`NIPBL MUTATED`
TCGA-B8-5162 TCGA-KL-8325 TCGA-KN-8428 TCGA-B8-5549 TCGA-BP-4163 TCGA-CW-5589 
        1.18        23.84        52.27         6.38        93.34        78.18 
TCGA-CZ-5985 TCGA-2Z-A9J8 TCGA-A4-7997 TCGA-A4-A48D TCGA-IA-A83S TCGA-IA-A83V 
       65.65        91.73        30.48        12.46        85.78        96.69 
TCGA-P4-A5E8 TCGA-SX-A71S TCGA-SX-A71U 
       42.94        49.45        44.61 

$`NIPBL WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-BP-4158 
       70.68       119.38       126.05        24.82        25.91       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       85.51        90.28       101.06        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        27.78        62.07         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
      119.64         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       66.31        74.66         1.35        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        69.21        58.75        14.66        63.39       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        67.96        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31        19.63        19.73        14.33        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T 
       73.25        25.22        16.80        19.99         2.04        88.24 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       14.07        47.90        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  NIPBL MUTATED NIPBL WILD-TYPE 
           1.18            0.07 
  NIPBL MUTATED NIPBL WILD-TYPE 
          96.69          194.79 
  NIPBL MUTATED NIPBL WILD-TYPE 
          49.45           36.85 
[1] "1.2 - 96.7 (49.5)"  "0.1 - 194.8 (36.9)"
[1] "hr=" "1.1"
D54V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NIPBL MUTATED         8        4         2        0
  NIPBL WILD-TYPE     391       85       173       93
D54V3, multiclass
           clus
vv          NIPBL MUTATED NIPBL WILD-TYPE
  STAGE I               8             391
  STAGE II              4              85
  STAGE III             2             173
  STAGE IV              0              93
[1] 4 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
  NIPBL MUTATED     8   5   1   0
  NIPBL WILD-TYPE 415 106 236  11
D54V4, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  T1             8             415
  T2             5             106
  T3             1             236
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NIPBL MUTATED     4   1   0
  NIPBL WILD-TYPE 289  39   5
D54V5, multiclass
    clus
vv   NIPBL MUTATED NIPBL WILD-TYPE
  N0             4             289
  N1             1              39
  N2             0               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"
D54V6, binary
                 cls
clus                0   1
  NIPBL MUTATED    10   0
  NIPBL WILD-TYPE 484  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED     10    0
  NIPBL WILD-TYPE  484   81
   clus
vv  NIPBL MUTATED NIPBL WILD-TYPE
  0            10             484
  1             0              81
[1] 2 2
[1] FALSE
D54V7, binary
                 cls
clus                0   1
  NIPBL MUTATED     3  12
  NIPBL WILD-TYPE 255 514
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      3   12
  NIPBL WILD-TYPE  255  514
        clus
vv       NIPBL MUTATED NIPBL WILD-TYPE
  FEMALE             3             255
  MALE              12             514
[1] 2 2
[1] FALSE
D54V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NIPBL MUTATED                    2                                 5
  NIPBL WILD-TYPE                 64                               431
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NIPBL MUTATED                                       8
  NIPBL WILD-TYPE                                   274
D54V9, multiclass
                                       clus
vv                                      NIPBL MUTATED NIPBL WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             8             274
[1] 3 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
D54V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NIPBL MUTATED                                  0     0
  NIPBL WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NIPBL MUTATED                           1    14
  NIPBL WILD-TYPE                        82   649
D54V12, multiclass
                                  clus
vv                                 NIPBL MUTATED NIPBL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                       14             649
[1] 4 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
  NIPBL MUTATED     0  13
  NIPBL WILD-TYPE  36 542
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NIPBL MUTATED      0   13
  NIPBL WILD-TYPE   36  542
                        clus
vv                       NIPBL MUTATED NIPBL WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO            13             542
[1] 2 2
[1] FALSE

Clustering(55) Variable = FAM47A MUTATION ANALYSIS
D55V1, survival
                  sevent
clus2                0   1
  FAM47A MUTATED     2   4
  FAM47A WILD-TYPE 576 198
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              774 
  FAM47A MUTATED FAM47A WILD-TYPE 
               4              198 
$`FAM47A MUTATED`
TCGA-BP-4164 TCGA-CZ-4865 TCGA-KN-8432 TCGA-CJ-4638 TCGA-CZ-5465 TCGA-MH-A560 
       32.61         5.46         2.50        14.17        84.30        30.38 

$`FAM47A WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
      111.02        94.72        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
      107.54        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO 
       19.73        17.75        12.49        35.38        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        46.55        73.22       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  FAM47A MUTATED FAM47A WILD-TYPE 
            2.50             0.07 
  FAM47A MUTATED FAM47A WILD-TYPE 
           84.30           194.79 
  FAM47A MUTATED FAM47A WILD-TYPE 
          22.275           37.235 
[1] "2.5 - 84.3 (22.3)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "4"  
D55V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  FAM47A MUTATED         2        1         2        1
  FAM47A WILD-TYPE     397       88       173       92
D55V3, multiclass
           clus
vv          FAM47A MUTATED FAM47A WILD-TYPE
  STAGE I                2              397
  STAGE II               1               88
  STAGE III              2              173
  STAGE IV               1               92
[1] 4 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
  FAM47A MUTATED     2   1   3   0
  FAM47A WILD-TYPE 421 110 234  11
D55V4, multiclass
    clus
vv   FAM47A MUTATED FAM47A WILD-TYPE
  T1              2              421
  T2              1              110
  T3              3              234
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM47A MUTATED     0   1   0
  FAM47A WILD-TYPE 293  39   5
D55V5, multiclass
[1] "Remove cluster labels:" "FAM47A MUTATED"        
clus
  FAM47A MUTATED FAM47A WILD-TYPE 
               1              337 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4904       TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3373       TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3451 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5400       TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-5159       TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-5551       TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4162 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4340       TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4351       TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4761       TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4787       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4960 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4989 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5198       TCGA-CJ-4639       TCGA-CJ-4640 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868       TCGA-CJ-4869 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874       TCGA-CJ-4876 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4890       TCGA-CJ-4892       TCGA-CJ-4900       TCGA-CJ-4918 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-5678       TCGA-CJ-6033       TCGA-CW-5585       TCGA-CW-5591 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CW-6087       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-Y8-A897 
"FAM47A WILD-TYPE" 
D55V6, binary
                  cls
clus                 0   1
  FAM47A MUTATED     3   1
  FAM47A WILD-TYPE 491  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      3    1
  FAM47A WILD-TYPE  491   80
   clus
vv  FAM47A MUTATED FAM47A WILD-TYPE
  0              3              491
  1              1               80
[1] 2 2
[1] FALSE
D55V7, binary
                  cls
clus                 0   1
  FAM47A MUTATED     5   1
  FAM47A WILD-TYPE 253 525
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      5    1
  FAM47A WILD-TYPE  253  525
        clus
vv       FAM47A MUTATED FAM47A WILD-TYPE
  FEMALE              5              253
  MALE                1              525
[1] 2 2
[1] FALSE
D55V8, continuous
[1] "Remove cluster labels:" "FAM47A MUTATED"        
clus
  FAM47A MUTATED FAM47A WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5469 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-V9-A7HT 
"FAM47A WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM47A MUTATED                    1                                 4
  FAM47A WILD-TYPE                 65                               432
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM47A MUTATED                                       1
  FAM47A WILD-TYPE                                   281
D55V9, multiclass
                                       clus
vv                                      FAM47A MUTATED FAM47A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              1              281
[1] 3 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
D55V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM47A MUTATED                                  0     0
  FAM47A WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM47A MUTATED                           0     5
  FAM47A WILD-TYPE                        83   658
D55V12, multiclass
                                  clus
vv                                 FAM47A MUTATED FAM47A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         5              658
[1] 4 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
  FAM47A MUTATED     0   4
  FAM47A WILD-TYPE  36 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      0    4
  FAM47A WILD-TYPE   36  551
                        clus
vv                       FAM47A MUTATED FAM47A WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(56) Variable = RHEB MUTATION ANALYSIS
D56V1, survival
                sevent
clus2              0   1
  RHEB MUTATED     2   1
  RHEB WILD-TYPE 576 201
  RHEB MUTATED RHEB WILD-TYPE 
             3            777 
  RHEB MUTATED RHEB WILD-TYPE 
             1            201 
$`RHEB MUTATED`
TCGA-CJ-4895 TCGA-CJ-5686 TCGA-Q2-A5QZ 
       39.45        67.00        14.07 

$`RHEB WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 
       48.53         0.53        34.39        14.30        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 
        5.33        61.97        56.91        68.38        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71R 
        6.61        99.12        92.58        16.01        50.60        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  RHEB MUTATED RHEB WILD-TYPE 
         14.07           0.07 
  RHEB MUTATED RHEB WILD-TYPE 
         67.00         194.79 
  RHEB MUTATED RHEB WILD-TYPE 
         39.45          36.95 
[1] "14.1 - 67.0 (39.5)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.4"
D56V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHEB MUTATED         1        0         1        1
  RHEB WILD-TYPE     398       89       174       92
D56V3, multiclass
           clus
vv          RHEB MUTATED RHEB WILD-TYPE
  STAGE I              1            398
  STAGE II             0             89
  STAGE III            1            174
  STAGE IV             1             92
[1] 4 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 422 111 235  11
D56V4, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  T1            1            422
  T2            0            111
  T3            2            235
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RHEB MUTATED     0   0   0
  RHEB WILD-TYPE 293  40   5
D56V5, multiclass
D56V6, binary
                cls
clus               0   1
  RHEB MUTATED     1   1
  RHEB WILD-TYPE 493  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      1    1
  RHEB WILD-TYPE  493   80
   clus
vv  RHEB MUTATED RHEB WILD-TYPE
  0            1            493
  1            1             80
[1] 2 2
[1] FALSE
D56V7, binary
                cls
clus               0   1
  RHEB MUTATED     2   1
  RHEB WILD-TYPE 256 525
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      2    1
  RHEB WILD-TYPE  256  525
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  FEMALE            2            256
  MALE              1            525
[1] 2 2
[1] FALSE
D56V8, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1            125 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7836     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4622 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5158     TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861 
"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-EU-5904     TCGA-EU-5905 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-EU-5906     TCGA-EU-5907     TCGA-2Z-A9JE     TCGA-2Z-A9JK 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-8630     TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-F9-A7Q0     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM     TCGA-G7-A8LB 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-A8LC     TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-IA-A40U 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537     TCGA-SX-A71R 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SP     TCGA-SX-A7SQ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-V9-A7HT 
"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                                   281
D56V9, 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            281
[1] 3 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:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    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-B8-5158     TCGA-B8-5164 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5550     TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-5P-A9K3     TCGA-5P-A9KE     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-A69E     TCGA-DW-7963 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     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-IA-A83S     TCGA-IA-A83V 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-Y8-A894     TCGA-Y8-A896 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-Y8-A8RY 
"RHEB WILD-TYPE" 
D56V11, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             66 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    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-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"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-7963     TCGA-F9-A97G     TCGA-G7-6793 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40U     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL     TCGA-SX-A7SM 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM     TCGA-UZ-A9PS 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-UZ-A9PX     TCGA-WN-A9G9     TCGA-WN-AB4C     TCGA-Y8-A894 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHEB MUTATED                                  0     0
  RHEB WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHEB MUTATED                           1     2
  RHEB WILD-TYPE                        82   661
D56V12, multiclass
                                  clus
vv                                 RHEB MUTATED RHEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   1             82
  WHITE                                       2            661
[1] 4 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
  RHEB MUTATED     0   3
  RHEB WILD-TYPE  36 552
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      0    3
  RHEB WILD-TYPE   36  552
                        clus
vv                       RHEB MUTATED RHEB WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            3            552
[1] 2 2
[1] FALSE

Clustering(57) Variable = BRAF MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     4   1
  BRAF WILD-TYPE 574 201
  BRAF MUTATED BRAF WILD-TYPE 
             5            775 
  BRAF MUTATED BRAF WILD-TYPE 
             1            201 
$`BRAF MUTATED`
TCGA-B8-4143 TCGA-AL-3467 TCGA-B1-5398 TCGA-UZ-A9PP TCGA-WN-A9G9 
       23.31        70.19        41.13        98.96        26.01 

$`BRAF WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       71.41        73.84       149.16       105.37       123.09       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 
        1.68        31.96        21.30        31.66        21.57        12.00 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       12.46         9.63        66.71        62.66        67.73         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS 
       26.20       117.40       103.63       125.29        37.35        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  BRAF MUTATED BRAF WILD-TYPE 
         23.31           0.07 
  BRAF MUTATED BRAF WILD-TYPE 
         98.96         194.79 
  BRAF MUTATED BRAF WILD-TYPE 
         41.13          36.95 
[1] "23.3 - 99.0 (41.1)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.5"
D57V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BRAF MUTATED         2        0         1        1
  BRAF WILD-TYPE     397       89       174       92
D57V3, multiclass
           clus
vv          BRAF MUTATED BRAF WILD-TYPE
  STAGE I              2            397
  STAGE II             0             89
  STAGE III            1            174
  STAGE IV             1             92
[1] 4 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
  BRAF MUTATED     3   0   2   0
  BRAF WILD-TYPE 420 111 235  11
D57V4, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T1            3            420
  T2            0            111
  T3            2            235
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BRAF MUTATED     2   0   0
  BRAF WILD-TYPE 291  40   5
D57V5, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             2            336 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8329 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KO-8405     TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A3-3357     TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A3-3373     TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3451 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5092     TCGA-B0-5094 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5400     TCGA-B0-5692     TCGA-B0-5696     TCGA-B0-5697 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4330     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BP-5198     TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-4890     TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-A655     TCGA-B1-A656 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5893 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131     TCGA-F9-A8NY 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846     TCGA-GL-7966 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U     TCGA-IA-A40Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2     TCGA-KV-A74V 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-AAVL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP     TCGA-SX-A7SS 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX     TCGA-Y8-A897 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
D57V6, binary
                cls
clus               0   1
  BRAF MUTATED     2   1
  BRAF WILD-TYPE 492  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    1
  BRAF WILD-TYPE  492   80
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0            2            492
  1            1             80
[1] 2 2
[1] FALSE
D57V7, binary
                cls
clus               0   1
  BRAF MUTATED     2   3
  BRAF WILD-TYPE 256 523
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      2    3
  BRAF WILD-TYPE  256  523
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            2            256
  MALE              3            523
[1] 2 2
[1] FALSE
D57V8, continuous
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1            125 
    TCGA-KM-8439     TCGA-KM-8441     TCGA-KM-8442     TCGA-KO-8411 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4862     TCGA-DV-5565 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-2Z-A9JL     TCGA-2Z-A9JT 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-DW-7836     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-SX-A71W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SO     TCGA-UZ-A9PZ     TCGA-KM-8438     TCGA-KM-8440 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477     TCGA-KM-8639 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8434     TCGA-KO-8413     TCGA-AK-3428 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4622     TCGA-B8-5158 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CJ-6028     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-5456 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5458     TCGA-CZ-5465     TCGA-CZ-5469 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CZ-5982     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5906 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EU-5907     TCGA-2Z-A9JE     TCGA-2Z-A9JK     TCGA-2Z-A9JN 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y     TCGA-A4-7286 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8517     TCGA-A4-8518     TCGA-A4-8630 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-7963 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-F9-A7Q0 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-G7-A8LB     TCGA-G7-A8LC 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-A8LD     TCGA-G7-A8LE     TCGA-IA-A40U     TCGA-IA-A40X 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537     TCGA-Q2-A5QZ     TCGA-SX-A71R 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A71V     TCGA-SX-A7SL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SN     TCGA-SX-A7SP     TCGA-SX-A7SQ 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-SX-A7SU     TCGA-UZ-A9PL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-V9-A7HT 
"BRAF WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  BRAF MUTATED                    0                                 1
  BRAF WILD-TYPE                 66                               435
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  BRAF MUTATED                                       4
  BRAF WILD-TYPE                                   278
D57V9, multiclass
                                       clus
vv                                      BRAF MUTATED BRAF WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            4            278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1             93 
    TCGA-B8-4621     TCGA-2Z-A9JD     TCGA-2Z-A9JQ     TCGA-5P-A9JU 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-A44B     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7838 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-GL-A59T     TCGA-IZ-A6M8     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-AK-3445 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3451     TCGA-B8-4146     TCGA-B8-5158     TCGA-B8-5164 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B8-5550     TCGA-2Z-A9J2     TCGA-2Z-A9J5     TCGA-2Z-A9J7 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9J8     TCGA-2Z-A9JI     TCGA-2Z-A9JK     TCGA-2Z-A9JM 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-5P-A9K3     TCGA-5P-A9KE     TCGA-A4-8310     TCGA-A4-A48D 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4115 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A69E     TCGA-DW-7963 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-F9-A97G     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD     TCGA-G7-A8LE 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI     TCGA-HE-A5NJ 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IA-A83S     TCGA-IA-A83V 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E7     TCGA-P4-A5EB 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-Y8-A894     TCGA-Y8-A896 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A8RY 
"BRAF WILD-TYPE" 
D57V11, continuous
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             1             66 
    TCGA-2Z-A9JD     TCGA-DW-5561     TCGA-PJ-A5Z9     TCGA-PJ-A8JU 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A71W     TCGA-UZ-A9PO     TCGA-UZ-A9PR     TCGA-Y8-A8RZ 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AK-3445     TCGA-AK-3451     TCGA-B8-5158     TCGA-B8-5550 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9J3     TCGA-2Z-A9J7     TCGA-2Z-A9J8     TCGA-2Z-A9JI 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-2Z-A9JN     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4114     TCGA-B9-4117 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-7963     TCGA-F9-A97G     TCGA-G7-6793 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LB     TCGA-G7-A8LD 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G7-A8LE     TCGA-GL-7773     TCGA-GL-A9DD     TCGA-HE-A5NI 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-IA-A40U     TCGA-MH-A854     TCGA-MH-A856     TCGA-P4-A5E6 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Q2-A5QZ     TCGA-SX-A71S     TCGA-SX-A71U     TCGA-SX-A7SL 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-SX-A7SM     TCGA-SX-A7SR     TCGA-SX-A7SS     TCGA-UZ-A9PM 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-UZ-A9PS     TCGA-UZ-A9PX     TCGA-WN-AB4C     TCGA-Y8-A894 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-Y8-A896     TCGA-Y8-A8RY 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BRAF MUTATED                                  0     0
  BRAF WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED                           0     5
  BRAF WILD-TYPE                        83   658
D57V12, multiclass
                                  clus
vv                                 BRAF MUTATED BRAF WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                       5            658
[1] 4 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
  BRAF MUTATED     0   5
  BRAF WILD-TYPE  36 550
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      0    5
  BRAF WILD-TYPE   36  550
                        clus
vv                       BRAF MUTATED BRAF WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            5            550
[1] 2 2
[1] FALSE

Clustering(58) Variable = MLL3 MUTATION ANALYSIS
D58V1, survival
                sevent
clus2              0   1
  MLL3 MUTATED    32  10
  MLL3 WILD-TYPE 546 192
  MLL3 MUTATED MLL3 WILD-TYPE 
            42            738 
  MLL3 MUTATED MLL3 WILD-TYPE 
            10            192 
$`MLL3 MUTATED`
TCGA-KM-8442 TCGA-BP-4164 TCGA-BP-4976 TCGA-AL-A5DJ TCGA-DW-7840 TCGA-PJ-A5Z8 
       47.24        32.61        53.65        49.25         3.75        19.73 
TCGA-KL-8326 TCGA-KL-8333 TCGA-KM-8438 TCGA-KM-8440 TCGA-KN-8418 TCGA-KN-8424 
      109.22        98.33       151.96        44.91       129.37        65.19 
TCGA-KN-8432 TCGA-KO-8406 TCGA-A3-3370 TCGA-A3-3376 TCGA-B0-4810 TCGA-B0-4945 
        2.50       103.40        74.76        55.76        15.72        70.52 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B2-5633 TCGA-BP-4756 TCGA-CJ-5678 
       21.86        52.08        15.95        31.66        12.30        18.87 
TCGA-CJ-5683 TCGA-CZ-4857 TCGA-CZ-5986 TCGA-5P-A9KA TCGA-A4-7997 TCGA-B3-4104 
       62.10        47.08        12.26        12.99        30.48        34.49 
TCGA-B9-4114 TCGA-B9-A5W8 TCGA-B9-A8YI TCGA-BQ-5893 TCGA-BQ-7051 TCGA-G7-A4TM 
       28.18        17.23        12.30         7.92        50.40        25.25 
TCGA-GL-A9DD TCGA-P4-A5E7 TCGA-Q2-A5QZ TCGA-UZ-A9PS TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       11.21        87.09        14.07        71.24        51.35        31.73 

$`MLL3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3358 
      102.81        28.11        23.28        28.80       130.13        42.97 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       94.72        80.68        74.17        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 
       11.64        20.38        37.25         6.94        61.51        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 
       31.27        63.25        26.93        27.65       108.56       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       23.90        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       16.34        12.13        29.26        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 
        6.74        38.07       153.73        23.84       137.06        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       28.80        54.74        62.37        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
       31.33        23.47        87.91        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
        3.55         0.99        52.27        87.12        19.33        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      100.47        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3374 
       45.53        88.37        51.25        74.63        53.29        43.20 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       65.52        20.28       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       73.68        68.61       109.51        94.19        46.78        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00        65.10         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 
       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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5100 TCGA-B0-5102 
       15.09        10.95         8.05         2.24        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57        12.00         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        11.31        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 
       10.82         5.33        61.97        56.91        68.38        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
      133.71        25.71        22.32        25.25        18.15       122.83 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 
       74.66         1.35        83.90        18.77        25.45        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 
       67.96        65.65        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       43.04        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        30.58 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 
       43.99        22.06         0.16        14.86        17.49        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-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       61.28        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LC 
       71.44        25.15        20.52        25.84        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
        1.05        12.43        12.89        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       20.25        17.62        31.13        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71R 
        6.61        99.12        92.58        16.01        50.60        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        47.47        65.13       110.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  MLL3 MUTATED MLL3 WILD-TYPE 
          2.50           0.07 
  MLL3 MUTATED MLL3 WILD-TYPE 
        151.96         194.79 
  MLL3 MUTATED MLL3 WILD-TYPE 
         33.55          37.12 
[1] "2.5 - 152.0 (33.5)" "0.1 - 194.8 (37.1)"
[1] "hr=" "1.1"
D58V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MLL3 MUTATED        19       10         8        3
  MLL3 WILD-TYPE     380       79       167       90
D58V3, multiclass
           clus
vv          MLL3 MUTATED MLL3 WILD-TYPE
  STAGE I             19            380
  STAGE II            10             79
  STAGE III            8            167
  STAGE IV             3             90
[1] 4 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    20  12  10   0
  MLL3 WILD-TYPE 403  99 227  11
D58V4, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  T1           20            403
  T2           12             99
  T3           10            227
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MLL3 MUTATED    16   2   0
  MLL3 WILD-TYPE 277  38   5
D58V5, multiclass
    clus
vv   MLL3 MUTATED MLL3 WILD-TYPE
  N0           16            277
  N1            2             38
  N2            0              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"
D58V6, binary
                cls
clus               0   1
  MLL3 MUTATED    21   3
  MLL3 WILD-TYPE 473  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     21    3
  MLL3 WILD-TYPE  473   78
   clus
vv  MLL3 MUTATED MLL3 WILD-TYPE
  0           21            473
  1            3             78
[1] 2 2
[1] FALSE
D58V7, binary
                cls
clus               0   1
  MLL3 MUTATED    18  24
  MLL3 WILD-TYPE 240 502
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED     18   24
  MLL3 WILD-TYPE  240  502
        clus
vv       MLL3 MUTATED MLL3 WILD-TYPE
  FEMALE           18            240
  MALE             24            502
[1] 2 2
[1] FALSE
D58V8, 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                                      18
  MLL3 WILD-TYPE                                   264
D58V9, multiclass
                                       clus
vv                                      MLL3 MUTATED MLL3 WILD-TYPE
  KIDNEY CHROMOPHOBE                               9             57
  KIDNEY CLEAR CELL RENAL CARCINOMA               15            421
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           18            264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MLL3 MUTATED                                  0     1
  MLL3 WILD-TYPE                                2    13
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MLL3 MUTATED                          12    28
  MLL3 WILD-TYPE                        71   635
D58V12, multiclass
                                  clus
vv                                 MLL3 MUTATED MLL3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             13
  BLACK OR AFRICAN AMERICAN                  12             71
  WHITE                                      28            635
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                cls
clus               0   1
  MLL3 MUTATED     1  32
  MLL3 WILD-TYPE  35 523
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL3 MUTATED      1   32
  MLL3 WILD-TYPE   35  523
                        clus
vv                       MLL3 MUTATED MLL3 WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           32            523
[1] 2 2
[1] FALSE

Clustering(59) Variable = ANK3 MUTATION ANALYSIS
D59V1, survival
                sevent
clus2              0   1
  ANK3 MUTATED    20   2
  ANK3 WILD-TYPE 558 200
  ANK3 MUTATED ANK3 WILD-TYPE 
            22            758 
  ANK3 MUTATED ANK3 WILD-TYPE 
             2            200 
$`ANK3 MUTATED`
TCGA-BP-4995 TCGA-CW-6093 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-KM-8476 TCGA-AK-3456 
       45.07       103.43        19.73        17.75       123.12        37.58 
TCGA-B0-5098 TCGA-B4-5834 TCGA-BP-4161 TCGA-BP-4972 TCGA-BP-5192 TCGA-CJ-4869 
       52.08         1.25        90.28        49.38        23.47        83.97 
TCGA-CJ-4905 TCGA-CJ-4918 TCGA-EU-5906 TCGA-A4-A4ZT TCGA-B9-4117 TCGA-BQ-7048 
       49.18         3.06         6.77        16.96         0.46        93.34 
TCGA-EV-5901 TCGA-HE-7130 TCGA-MH-A854 TCGA-Y8-A894 
       34.19        58.19        17.62        18.64 

$`ANK3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 
       61.51        53.65        25.81        27.22         5.82        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56       118.85        75.58        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       56.84        23.90        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.49        35.38        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       62.37       151.96        44.91        49.97        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-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        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-A3-3362 
       37.38        48.82        52.93        45.53        88.37        51.25 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 
       74.63        74.76        53.29        43.20        55.76        65.52 
TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        94.19        46.78        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       83.21        38.40        82.45        72.89        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5835 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       34.39        14.30        85.51       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5194 
       37.25        37.22        22.78        13.35        33.24        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        21.24        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 
       50.24        56.35        47.67        49.97        51.29        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       18.12         3.91         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        15.48        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         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-A57E 
       23.31        19.63        19.73        14.33        12.46         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
       20.61         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92         2.76       123.62        48.26        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 TCGA-EV-5903 
       79.86        80.88        51.19        74.60        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  ANK3 MUTATED ANK3 WILD-TYPE 
          0.46           0.07 
  ANK3 MUTATED ANK3 WILD-TYPE 
        123.12         194.79 
  ANK3 MUTATED ANK3 WILD-TYPE 
        35.885         36.985 
[1] "0.5 - 123.1 (35.9)" "0.1 - 194.8 (37.0)"
[1] "hr=" "2.8"
D59V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ANK3 MUTATED        15        1         4        1
  ANK3 WILD-TYPE     384       88       171       92
D59V3, multiclass
           clus
vv          ANK3 MUTATED ANK3 WILD-TYPE
  STAGE I             15            384
  STAGE II             1             88
  STAGE III            4            171
  STAGE IV             1             92
[1] 4 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
  ANK3 MUTATED    15   3   4   0
  ANK3 WILD-TYPE 408 108 233  11
D59V4, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  T1           15            408
  T2            3            108
  T3            4            233
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  ANK3 MUTATED     5   1   0
  ANK3 WILD-TYPE 288  39   5
D59V5, multiclass
    clus
vv   ANK3 MUTATED ANK3 WILD-TYPE
  N0            5            288
  N1            1             39
  N2            0              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"
D59V6, binary
                cls
clus               0   1
  ANK3 MUTATED    15   1
  ANK3 WILD-TYPE 479  80
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     15    1
  ANK3 WILD-TYPE  479   80
   clus
vv  ANK3 MUTATED ANK3 WILD-TYPE
  0           15            479
  1            1             80
[1] 2 2
[1] FALSE
D59V7, binary
                cls
clus               0   1
  ANK3 MUTATED    11  11
  ANK3 WILD-TYPE 247 515
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED     11   11
  ANK3 WILD-TYPE  247  515
        clus
vv       ANK3 MUTATED ANK3 WILD-TYPE
  FEMALE           11            247
  MALE             11            515
[1] 2 2
[1] FALSE
D59V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ANK3 MUTATED                    1                                12
  ANK3 WILD-TYPE                 65                               424
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ANK3 MUTATED                                       9
  ANK3 WILD-TYPE                                   273
D59V9, multiclass
                                       clus
vv                                      ANK3 MUTATED ANK3 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA               12            424
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            9            273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ANK3 MUTATED                                  0     0
  ANK3 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  ANK3 MUTATED                           4    17
  ANK3 WILD-TYPE                        79   646
D59V12, multiclass
                                  clus
vv                                 ANK3 MUTATED ANK3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   4             79
  WHITE                                      17            646
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                cls
clus               0   1
  ANK3 MUTATED     1  16
  ANK3 WILD-TYPE  35 539
[1] "tbl2"
                cls
clus             [,1] [,2]
  ANK3 MUTATED      1   16
  ANK3 WILD-TYPE   35  539
                        clus
vv                       ANK3 MUTATED ANK3 WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO           16            539
[1] 2 2
[1] FALSE

Clustering(60) Variable = EMG1 MUTATION ANALYSIS
D60V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 574 202
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            776 
  EMG1 MUTATED EMG1 WILD-TYPE 
             0            202 
$`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-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       82.45        72.89        12.13         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        37.22        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  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         36.950 
[1] "22.8 - 117.8 (67.4)" "0.1 - 194.8 (37.0)" 
[1] "hr="     "3300000"
D60V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EMG1 MUTATED         4        0         0        0
  EMG1 WILD-TYPE     395       89       175       93
D60V3, multiclass
           clus
vv          EMG1 MUTATED EMG1 WILD-TYPE
  STAGE I              4            395
  STAGE II             0             89
  STAGE III            0            175
  STAGE IV             0             93
[1] 4 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 419 111 237  11
D60V4, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T1            4            419
  T2            0            111
  T3            0            237
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EMG1 MUTATED     2   0   0
  EMG1 WILD-TYPE 291  40   5
D60V5, multiclass
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            336 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-KL-8326     TCGA-KL-8327     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-8340     TCGA-KL-8341     TCGA-KL-8342 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8405     TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3357     TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3373     TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A3-3387     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-3451     TCGA-AK-3456 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693     TCGA-B0-4703 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4814 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823     TCGA-B0-4824 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837     TCGA-B0-4838 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843     TCGA-B0-4846 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075     TCGA-B0-5077 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083     TCGA-B0-5084 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5085     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5699 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4330     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5198 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918     TCGA-CJ-5678 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-2Z-A9J1 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X     TCGA-4A-A93Y 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5893 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131     TCGA-F9-A8NY 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-F9-A97G     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-G7-A8LD     TCGA-GL-6846     TCGA-GL-7966 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U     TCGA-IA-A40Y 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2     TCGA-KV-A74V 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA     TCGA-P4-AAVL 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP     TCGA-SX-A7SS 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX     TCGA-Y8-A897 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
D60V6, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 490  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  490   81
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            490
  1            0             81
[1] 2 2
[1] FALSE
D60V7, binary
                cls
clus               0   1
  EMG1 MUTATED     1   3
  EMG1 WILD-TYPE 257 523
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      1    3
  EMG1 WILD-TYPE  257  523
        clus
vv       EMG1 MUTATED EMG1 WILD-TYPE
  FEMALE            1            257
  MALE              3            523
[1] 2 2
[1] FALSE
D60V8, 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                                   282
D60V9, 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            282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EMG1 MUTATED                                  0     0
  EMG1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED                           0     4
  EMG1 WILD-TYPE                        83   659
D60V12, multiclass
                                  clus
vv                                 EMG1 MUTATED EMG1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                       4            659
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                cls
clus               0   1
  EMG1 MUTATED     0   3
  EMG1 WILD-TYPE  36 552
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      0    3
  EMG1 WILD-TYPE   36  552
                        clus
vv                       EMG1 MUTATED EMG1 WILD-TYPE
  HISPANIC OR LATINO                0             36
  NOT HISPANIC OR LATINO            3            552
[1] 2 2
[1] FALSE

Clustering(61) Variable = LHX1 MUTATION ANALYSIS
D61V1, survival
                sevent
clus2              0   1
  LHX1 MUTATED     3   1
  LHX1 WILD-TYPE 575 201
  LHX1 MUTATED LHX1 WILD-TYPE 
             4            776 
  LHX1 MUTATED LHX1 WILD-TYPE 
             1            201 
$`LHX1 MUTATED`
TCGA-A4-7288 TCGA-KL-8325 TCGA-B8-4151 TCGA-CJ-5675 
       61.05        23.84        42.71       129.40 

$`LHX1 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       16.80        49.97        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-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-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  LHX1 MUTATED LHX1 WILD-TYPE 
         23.84           0.07 
  LHX1 MUTATED LHX1 WILD-TYPE 
        129.40         194.79 
  LHX1 MUTATED LHX1 WILD-TYPE 
         51.88          36.95 
[1] "23.8 - 129.4 (51.9)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "1.4"
D61V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  LHX1 MUTATED         0        2         1        0
  LHX1 WILD-TYPE     399       87       174       93
D61V3, multiclass
           clus
vv          LHX1 MUTATED LHX1 WILD-TYPE
  STAGE I              0            399
  STAGE II             2             87
  STAGE III            1            174
  STAGE IV             0             93
[1] 4 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
  LHX1 MUTATED     1   2   1   0
  LHX1 WILD-TYPE 422 109 236  11
D61V4, multiclass
    clus
vv   LHX1 MUTATED LHX1 WILD-TYPE
  T1            1            422
  T2            2            109
  T3            1            236
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  LHX1 MUTATED     1   0   0
  LHX1 WILD-TYPE 292  40   5
D61V5, multiclass
[1] "Remove cluster labels:" "LHX1 MUTATED"          
clus
  LHX1 MUTATED LHX1 WILD-TYPE 
             1            337 
    TCGA-KL-8328     TCGA-KL-8339     TCGA-KN-8430     TCGA-A3-3358 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3450     TCGA-B0-5088     TCGA-B0-5691 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5698     TCGA-B8-4621 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4331     TCGA-BP-4342 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4799     TCGA-BP-4986     TCGA-BP-4988 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5191     TCGA-BP-5199 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4891     TCGA-CJ-4894 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-6030     TCGA-CZ-4854     TCGA-CZ-4856 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-5P-A9JU     TCGA-A4-A5Y1     TCGA-B1-A47O     TCGA-B1-A657 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5892     TCGA-BQ-7056     TCGA-IA-A83W 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-Y8-A8RZ     TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8329 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8340     TCGA-KL-8341     TCGA-KL-8342 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345     TCGA-KL-8346 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418     TCGA-KN-8419 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423     TCGA-KN-8424 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428     TCGA-KN-8429 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KO-8405     TCGA-KO-8406     TCGA-KO-8407     TCGA-KO-8408 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3313 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-A3-3357     TCGA-A3-3362     TCGA-A3-3367     TCGA-A3-3370 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-A3-3373     TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3385 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3451 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5092     TCGA-B0-5094 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5400     TCGA-B0-5692     TCGA-B0-5696     TCGA-B0-5697 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4154     TCGA-B8-4619 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4159     TCGA-BP-4162     TCGA-BP-4163 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4330     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4960     TCGA-BP-4964 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4989     TCGA-BP-5007 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BP-5198     TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CJ-4890     TCGA-CJ-4892     TCGA-CJ-4900     TCGA-CJ-4918 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CW-6087     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-2Z-A9J1     TCGA-2Z-A9JO     TCGA-4A-A93W     TCGA-4A-A93X 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-4A-A93Y     TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A7UZ     TCGA-AL-3466     TCGA-AL-3472 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-B1-A656     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-DW-7963     TCGA-DZ-6131 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-F9-A8NY     TCGA-F9-A97G     TCGA-G7-6789     TCGA-G7-6793 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-G7-A8LD     TCGA-GL-6846 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-GL-A9DC     TCGA-IA-A40U 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-6720     TCGA-J7-8537     TCGA-J7-A8I2 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-KV-A74V     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-P4-AAVL     TCGA-SX-A71R     TCGA-SX-A7SM     TCGA-SX-A7SP 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-SX-A7SS     TCGA-UN-AAZ9     TCGA-UZ-A9PM     TCGA-UZ-A9PX 
"LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" "LHX1 WILD-TYPE" 
    TCGA-Y8-A897 
"LHX1 WILD-TYPE" 
D61V6, binary
                cls
clus               0   1
  LHX1 MUTATED     3   0
  LHX1 WILD-TYPE 491  81
[1] "tbl2"
                cls
clus             [,1] [,2]
  LHX1 MUTATED      3    0
  LHX1 WILD-TYPE  491   81
   clus
vv  LHX1 MUTATED LHX1 WILD-TYPE
  0            3            491
  1            0             81
[1] 2 2
[1] FALSE
D61V7, binary
                cls
clus               0   1
  LHX1 MUTATED     3   1
  LHX1 WILD-TYPE 255 525
[1] "tbl2"
                cls
clus             [,1] [,2]
  LHX1 MUTATED      3    1
  LHX1 WILD-TYPE  255  525
        clus
vv       LHX1 MUTATED LHX1 WILD-TYPE
  FEMALE            3            255
  MALE              1            525
[1] 2 2
[1] FALSE
D61V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  LHX1 MUTATED                    1                                 2
  LHX1 WILD-TYPE                 65                               434
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  LHX1 MUTATED                                       1
  LHX1 WILD-TYPE                                   281
D61V9, multiclass
                                       clus
vv                                      LHX1 MUTATED LHX1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                2            434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  LHX1 MUTATED                                  0     0
  LHX1 WILD-TYPE                                2    14
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  LHX1 MUTATED                           0     4
  LHX1 WILD-TYPE                        83   659
D61V12, multiclass
                                  clus
vv                                 LHX1 MUTATED LHX1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             14
  BLACK OR AFRICAN AMERICAN                   0             83
  WHITE                                       4            659
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                cls
clus               0   1
  LHX1 MUTATED     1   2
  LHX1 WILD-TYPE  35 553
[1] "tbl2"
                cls
clus             [,1] [,2]
  LHX1 MUTATED      1    2
  LHX1 WILD-TYPE   35  553
                        clus
vv                       LHX1 MUTATED LHX1 WILD-TYPE
  HISPANIC OR LATINO                1             35
  NOT HISPANIC OR LATINO            2            553
[1] 2 2
[1] FALSE

Clustering(62) Variable = SCARB2 MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  SCARB2 MUTATED     1   3
  SCARB2 WILD-TYPE 577 199
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               4              776 
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               3              199 
$`SCARB2 MUTATED`
TCGA-CJ-6027 TCGA-BP-5176 TCGA-CZ-4861 TCGA-CZ-5451 
      118.85        52.27        14.66        63.42 

$`SCARB2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       27.65       108.56        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
       79.30         2.04        74.20        30.64         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       58.75        63.39       107.41        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  SCARB2 MUTATED SCARB2 WILD-TYPE 
           14.66             0.07 
  SCARB2 MUTATED SCARB2 WILD-TYPE 
          118.85           194.79 
  SCARB2 MUTATED SCARB2 WILD-TYPE 
          57.845           36.950 
[1] "14.7 - 118.8 (57.8)" "0.1 - 194.8 (37.0)" 
[1] "hr=" "2.1"
D62V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SCARB2 MUTATED         2        2         0        0
  SCARB2 WILD-TYPE     397       87       175       93
D62V3, multiclass
           clus
vv          SCARB2 MUTATED SCARB2 WILD-TYPE
  STAGE I                2              397
  STAGE II               2               87
  STAGE III              0              175
  STAGE IV               0               93
[1] 4 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
  SCARB2 MUTATED     2   2   0   0
  SCARB2 WILD-TYPE 421 109 237  11
D62V4, multiclass
    clus
vv   SCARB2 MUTATED SCARB2 WILD-TYPE
  T1              2              421
  T2              2              109
  T3              0              237
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SCARB2 MUTATED     1   0   0
  SCARB2 WILD-TYPE 292  40   5
D62V5, multiclass
[1] "Remove cluster labels:" "SCARB2 MUTATED"        
clus
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               1              337 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CJ-4904       TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A3-3373       TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3451 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5400       TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-5159       TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-5551       TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4162 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4340       TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4351       TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4761       TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4787       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4960 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4989 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5198       TCGA-CJ-4638       TCGA-CJ-4639 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4892       TCGA-CJ-4900 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6033       TCGA-CW-5585 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4857       TCGA-CZ-4859 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-4863       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93X 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466       TCGA-AL-3472 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B1-A656       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-Y8-A897 
"SCARB2 WILD-TYPE" 
D62V6, binary
                  cls
clus                 0   1
  SCARB2 MUTATED     4   0
  SCARB2 WILD-TYPE 490  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARB2 MUTATED      4    0
  SCARB2 WILD-TYPE  490   81
   clus
vv  SCARB2 MUTATED SCARB2 WILD-TYPE
  0              4              490
  1              0               81
[1] 2 2
[1] FALSE
D62V7, binary
                  cls
clus                 0   1
  SCARB2 MUTATED     1   3
  SCARB2 WILD-TYPE 257 523
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARB2 MUTATED      1    3
  SCARB2 WILD-TYPE  257  523
        clus
vv       SCARB2 MUTATED SCARB2 WILD-TYPE
  FEMALE              1              257
  MALE                3              523
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "SCARB2 MUTATED"        
clus
  SCARB2 MUTATED SCARB2 WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-5456 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465       TCGA-CZ-5469 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5906 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK       TCGA-2Z-A9JN 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" "SCARB2 WILD-TYPE" 
      TCGA-V9-A7HT 
"SCARB2 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SCARB2 MUTATED                    0                                 4
  SCARB2 WILD-TYPE                 66                               432
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SCARB2 MUTATED                                       0
  SCARB2 WILD-TYPE                                   282
D62V9, multiclass
                                       clus
vv                                      SCARB2 MUTATED SCARB2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              432
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              0              282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SCARB2 MUTATED                                  0     0
  SCARB2 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SCARB2 MUTATED                           0     4
  SCARB2 WILD-TYPE                        83   659
D62V12, multiclass
                                  clus
vv                                 SCARB2 MUTATED SCARB2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         4              659
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                  cls
clus                 0   1
  SCARB2 MUTATED     0   1
  SCARB2 WILD-TYPE  36 554
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SCARB2 MUTATED      0    1
  SCARB2 WILD-TYPE   36  554
                        clus
vv                       SCARB2 MUTATED SCARB2 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              1              554
[1] 2 2
[1] FALSE

Clustering(63) Variable = C1ORF25 MUTATION ANALYSIS
D63V1, survival
                   sevent
clus2                 0   1
  C1ORF25 MUTATED     4   2
  C1ORF25 WILD-TYPE 574 200
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                6               774 
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                2               200 
$`C1ORF25 MUTATED`
TCGA-5P-A9JU TCGA-KO-8404 TCGA-B0-5121 TCGA-B4-5836 TCGA-CZ-5467 TCGA-IZ-8195 
       12.26        10.68        48.82         4.64         2.40        22.26 

$`C1ORF25 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        16.18        22.49        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       59.08       115.00        42.35       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       38.43        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
       10.85        10.22        21.76        84.30        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       14.63        22.78        62.63        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
        4.18         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
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        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         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-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       96.69        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       87.09        42.94         6.61        99.12        92.58        16.01 
TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
             2.40              0.07 
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
            48.82            194.79 
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
           11.470            37.235 
[1] "2.4 - 48.8 (11.5)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "3.4"
D63V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  C1ORF25 MUTATED         2        1         2        1
  C1ORF25 WILD-TYPE     397       88       173       92
D63V3, multiclass
           clus
vv          C1ORF25 MUTATED C1ORF25 WILD-TYPE
  STAGE I                 2               397
  STAGE II                1                88
  STAGE III               2               173
  STAGE IV                1                92
[1] 4 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
  C1ORF25 MUTATED     2   1   2   1
  C1ORF25 WILD-TYPE 421 110 235  10
D63V4, multiclass
    clus
vv   C1ORF25 MUTATED C1ORF25 WILD-TYPE
  T1               2               421
  T2               1               110
  T3               2               235
  T4               1                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
  C1ORF25 MUTATED     4   0   0
  C1ORF25 WILD-TYPE 289  40   5
D63V5, multiclass
    clus
vv   C1ORF25 MUTATED C1ORF25 WILD-TYPE
  N0               4               289
  N1               0                40
  N2               0                 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"
D63V6, binary
                   cls
clus                  0   1
  C1ORF25 MUTATED     4   0
  C1ORF25 WILD-TYPE 490  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF25 MUTATED      4    0
  C1ORF25 WILD-TYPE  490   81
   clus
vv  C1ORF25 MUTATED C1ORF25 WILD-TYPE
  0               4               490
  1               0                81
[1] 2 2
[1] FALSE
D63V7, binary
                   cls
clus                  0   1
  C1ORF25 MUTATED     2   4
  C1ORF25 WILD-TYPE 256 522
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF25 MUTATED      2    4
  C1ORF25 WILD-TYPE  256  522
        clus
vv       C1ORF25 MUTATED C1ORF25 WILD-TYPE
  FEMALE               2               256
  MALE                 4               522
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "C1ORF25 MUTATED"       
clus
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                2               124 
       TCGA-KM-8439        TCGA-KM-8441        TCGA-KM-8442        TCGA-KO-8411 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4862        TCGA-DV-5565 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-2Z-A9JL        TCGA-2Z-A9JT 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-SX-A71W        TCGA-SX-A7SO 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-UZ-A9PZ        TCGA-KM-8438        TCGA-KM-8440        TCGA-KM-8443 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-KM-8476        TCGA-KM-8477        TCGA-KM-8639        TCGA-KN-8429 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-KN-8434        TCGA-KO-8413        TCGA-AK-3428        TCGA-AK-3430 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B8-4143        TCGA-B8-4622        TCGA-B8-5158        TCGA-CJ-6028 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-CZ-4858        TCGA-CZ-4861        TCGA-CZ-5456        TCGA-CZ-5457 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-CZ-5458        TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5906        TCGA-EU-5907 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-2Z-A9JE        TCGA-2Z-A9JK        TCGA-2Z-A9JN        TCGA-4A-A93W 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-4A-A93X        TCGA-4A-A93Y        TCGA-A4-7286        TCGA-A4-7828 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-A4-8098        TCGA-A4-8310        TCGA-A4-8311        TCGA-A4-8312 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-A4-8517        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A48D 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-A4-A6HP        TCGA-AL-3466        TCGA-DW-7963        TCGA-EV-5901 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-F9-A7Q0        TCGA-G7-6789 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-G7-A8LB        TCGA-G7-A8LC        TCGA-G7-A8LD 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ        TCGA-SX-A71R        TCGA-SX-A71S 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A71V        TCGA-SX-A7SL        TCGA-SX-A7SM 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-SX-A7SN        TCGA-SX-A7SP        TCGA-SX-A7SQ        TCGA-SX-A7SR 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-SX-A7SU        TCGA-UZ-A9PL        TCGA-V9-A7HT 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  C1ORF25 MUTATED                    1                                 3
  C1ORF25 WILD-TYPE                 65                               433
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  C1ORF25 MUTATED                                       2
  C1ORF25 WILD-TYPE                                   280
D63V9, multiclass
                                       clus
vv                                      C1ORF25 MUTATED C1ORF25 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   3               433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
[1] "Remove cluster labels:" "C1ORF25 MUTATED"       
clus
  C1ORF25 MUTATED C1ORF25 WILD-TYPE 
                1                93 
       TCGA-B8-4621        TCGA-2Z-A9JD        TCGA-2Z-A9JQ        TCGA-B9-A44B 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-PJ-A5Z9        TCGA-PJ-A8JU        TCGA-SX-A71W 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ        TCGA-KL-8324 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416        TCGA-AK-3445        TCGA-AK-3451 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B8-4146        TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-5P-A9KE        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4117 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896 
"C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" "C1ORF25 WILD-TYPE" 
       TCGA-Y8-A8RY 
"C1ORF25 WILD-TYPE" 
D63V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  C1ORF25 MUTATED                                  0     0
  C1ORF25 WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  C1ORF25 MUTATED                           0     6
  C1ORF25 WILD-TYPE                        83   657
D63V12, multiclass
                                  clus
vv                                 C1ORF25 MUTATED C1ORF25 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                14
  BLACK OR AFRICAN AMERICAN                      0                83
  WHITE                                          6               657
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                   cls
clus                  0   1
  C1ORF25 MUTATED     0   6
  C1ORF25 WILD-TYPE  36 549
[1] "tbl2"
                   cls
clus                [,1] [,2]
  C1ORF25 MUTATED      0    6
  C1ORF25 WILD-TYPE   36  549
                        clus
vv                       C1ORF25 MUTATED C1ORF25 WILD-TYPE
  HISPANIC OR LATINO                   0                36
  NOT HISPANIC OR LATINO               6               549
[1] 2 2
[1] FALSE

Clustering(64) Variable = KDELR3 MUTATION ANALYSIS
D64V1, survival
                  sevent
clus2                0   1
  KDELR3 MUTATED     4   3
  KDELR3 WILD-TYPE 574 199
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               7              773 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               3              199 
$`KDELR3 MUTATED`
TCGA-KN-8428 TCGA-KO-8404 TCGA-CJ-4902 TCGA-CZ-5984 TCGA-5P-A9JY TCGA-A4-7915 
       52.27        10.68        49.97        67.96        49.58         0.23 
TCGA-GL-8500 
       27.65 

$`KDELR3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55         0.99        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       59.08       115.00        42.35       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-5985 
        2.40         1.94        31.10        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
        5.29         0.13        12.82        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        15.48        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         7.82        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-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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        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-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         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-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
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-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94         6.61        99.12        92.58        16.01        50.60 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  KDELR3 MUTATED KDELR3 WILD-TYPE 
            0.23             0.07 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
           67.96           194.79 
  KDELR3 MUTATED KDELR3 WILD-TYPE 
           49.58            36.95 
[1] "0.2 - 68.0 (49.6)"  "0.1 - 194.8 (37.0)"
[1] "hr=" "1.9"
D64V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  KDELR3 MUTATED         2        2         1        1
  KDELR3 WILD-TYPE     397       87       174       92
D64V3, multiclass
           clus
vv          KDELR3 MUTATED KDELR3 WILD-TYPE
  STAGE I                2              397
  STAGE II               2               87
  STAGE III              1              174
  STAGE IV               1               92
[1] 4 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   3   1   1
  KDELR3 WILD-TYPE 421 108 236  10
D64V4, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  T1              2              421
  T2              3              108
  T3              1              236
  T4              1               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
  KDELR3 MUTATED     3   0   0
  KDELR3 WILD-TYPE 290  40   5
D64V5, multiclass
    clus
vv   KDELR3 MUTATED KDELR3 WILD-TYPE
  N0              3              290
  N1              0               40
  N2              0                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"
D64V6, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     2   0
  KDELR3 WILD-TYPE 492  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      2    0
  KDELR3 WILD-TYPE  492   81
   clus
vv  KDELR3 MUTATED KDELR3 WILD-TYPE
  0              2              492
  1              0               81
[1] 2 2
[1] FALSE
D64V7, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     1   6
  KDELR3 WILD-TYPE 257 520
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      1    6
  KDELR3 WILD-TYPE  257  520
        clus
vv       KDELR3 MUTATED KDELR3 WILD-TYPE
  FEMALE              1              257
  MALE                6              520
[1] 2 2
[1] FALSE
D64V8, 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                                       3
  KDELR3 WILD-TYPE                                   279
D64V9, multiclass
                                       clus
vv                                      KDELR3 MUTATED KDELR3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
[1] "Remove cluster labels:" "KDELR3 MUTATED"        
clus
  KDELR3 MUTATED KDELR3 WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      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-B8-5158       TCGA-B8-5164       TCGA-B8-5550 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7       TCGA-2Z-A9J8 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM       TCGA-2Z-A9JN 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y       TCGA-5P-A9K3 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-5P-A9KE       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-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-GL-A9DD       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-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" "KDELR3 WILD-TYPE" 
      TCGA-Y8-A8RY 
"KDELR3 WILD-TYPE" 
D64V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDELR3 MUTATED                                  0     0
  KDELR3 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  KDELR3 MUTATED                           1     6
  KDELR3 WILD-TYPE                        82   657
D64V12, multiclass
                                  clus
vv                                 KDELR3 MUTATED KDELR3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     1               82
  WHITE                                         6              657
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                  cls
clus                 0   1
  KDELR3 MUTATED     0   6
  KDELR3 WILD-TYPE  36 549
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KDELR3 MUTATED      0    6
  KDELR3 WILD-TYPE   36  549
                        clus
vv                       KDELR3 MUTATED KDELR3 WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              6              549
[1] 2 2
[1] FALSE

Clustering(65) Variable = TTLL6 MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  TTLL6 MUTATED     3   1
  TTLL6 WILD-TYPE 575 201
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              4             776 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              1             201 
$`TTLL6 MUTATED`
TCGA-DV-5569 TCGA-KL-8325 TCGA-KO-8409 TCGA-B4-5844 
       11.67        23.84       104.55         0.23 

$`TTLL6 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07       153.73       109.22       137.06        90.48       108.62 
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-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        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-8410 TCGA-KO-8413 TCGA-KO-8414 
      103.40        92.71        16.67       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         5.46         0.36        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 
       54.90        53.42        27.78        62.07         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82         5.33        61.97        56.91        68.38 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-EU-5904 TCGA-EU-5905 
       12.26        14.63        22.78        62.63        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        6.77         4.18         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  TTLL6 MUTATED TTLL6 WILD-TYPE 
           0.23            0.07 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
         104.55          194.79 
  TTLL6 MUTATED TTLL6 WILD-TYPE 
         17.755          37.120 
[1] "0.2 - 104.5 (17.8)" "0.1 - 194.8 (37.1)"
[1] "hr=" "1.3"
D65V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TTLL6 MUTATED         1        3         0        0
  TTLL6 WILD-TYPE     398       86       175       93
D65V3, multiclass
           clus
vv          TTLL6 MUTATED TTLL6 WILD-TYPE
  STAGE I               1             398
  STAGE II              3              86
  STAGE III             0             175
  STAGE IV              0              93
[1] 4 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   3   0   0
  TTLL6 WILD-TYPE 422 108 237  11
D65V4, multiclass
    clus
vv   TTLL6 MUTATED TTLL6 WILD-TYPE
  T1             1             422
  T2             3             108
  T3             0             237
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TTLL6 MUTATED     2   0   0
  TTLL6 WILD-TYPE 291  40   5
D65V5, multiclass
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              2             336 
     TCGA-KL-8328      TCGA-KL-8339      TCGA-KN-8430      TCGA-A3-3358 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3450      TCGA-B0-5088      TCGA-B0-5691 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5698      TCGA-B8-4621 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4160      TCGA-BP-4331      TCGA-BP-4342 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4799      TCGA-BP-4986      TCGA-BP-4988 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5191      TCGA-BP-5199 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4891      TCGA-CJ-4894 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-6030      TCGA-CZ-4854      TCGA-CZ-4856 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-5P-A9JU      TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-Y8-A8RZ      TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8329 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418      TCGA-KN-8419 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423      TCGA-KN-8424 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KO-8410      TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KO-8416      TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A3-3331      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429      TCGA-AK-3430 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3451      TCGA-AK-3456 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4690      TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4710      TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4816      TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5085      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5699 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      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-B8-4148 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159      TCGA-B8-5163 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545      TCGA-B8-5546 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5553 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4159      TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4343 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351      TCGA-BP-4352 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761      TCGA-BP-4768 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787      TCGA-BP-4797 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4798      TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-4985      TCGA-BP-4989      TCGA-BP-5007      TCGA-BP-5010 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5198 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4900      TCGA-CJ-4918      TCGA-CJ-5678 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-5451 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456      TCGA-CZ-5467 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984      TCGA-CZ-5985 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-2Z-A9J1 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93X      TCGA-4A-A93Y 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A7UZ      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5893 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131      TCGA-F9-A8NY 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846      TCGA-GL-7966 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U      TCGA-IA-A40Y 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2      TCGA-KV-A74V 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA      TCGA-P4-AAVL 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP      TCGA-SX-A7SS 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX      TCGA-Y8-A897 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
D65V6, binary
                 cls
clus                0   1
  TTLL6 MUTATED     4   0
  TTLL6 WILD-TYPE 490  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      4    0
  TTLL6 WILD-TYPE  490   81
   clus
vv  TTLL6 MUTATED TTLL6 WILD-TYPE
  0             4             490
  1             0              81
[1] 2 2
[1] FALSE
D65V7, binary
                 cls
clus                0   1
  TTLL6 MUTATED     3   1
  TTLL6 WILD-TYPE 255 525
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      3    1
  TTLL6 WILD-TYPE  255  525
        clus
vv       TTLL6 MUTATED TTLL6 WILD-TYPE
  FEMALE             3             255
  MALE               1             525
[1] 2 2
[1] FALSE
D65V8, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              2             124 
     TCGA-KM-8439      TCGA-KM-8441      TCGA-KM-8442      TCGA-KO-8411 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4862      TCGA-DV-5565 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5574      TCGA-DV-5575 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DV-5576      TCGA-2Z-A9JL      TCGA-2Z-A9JT      TCGA-5P-A9JU 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7836 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-SX-A71W      TCGA-SX-A7SO 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-UZ-A9PZ      TCGA-KM-8438      TCGA-KM-8440      TCGA-KM-8443 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639      TCGA-KN-8429 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-KN-8434      TCGA-KO-8413      TCGA-AK-3428      TCGA-AK-3430 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4622      TCGA-B8-5158      TCGA-CJ-6028 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-CZ-5458      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906      TCGA-EU-5907 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9JE      TCGA-2Z-A9JK      TCGA-2Z-A9JN      TCGA-4A-A93W 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-4A-A93X      TCGA-4A-A93Y      TCGA-A4-7286      TCGA-A4-7828 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-8517      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A48D 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-7963      TCGA-EV-5901 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A7Q0      TCGA-G7-6789 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-G7-A8LB      TCGA-G7-A8LC      TCGA-G7-A8LD 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ      TCGA-SX-A71R      TCGA-SX-A71S 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71U      TCGA-SX-A71V      TCGA-SX-A7SL      TCGA-SX-A7SM 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A7SN      TCGA-SX-A7SP      TCGA-SX-A7SQ      TCGA-SX-A7SR 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-SX-A7SU      TCGA-UZ-A9PL      TCGA-V9-A7HT 
"TTLL6 WILD-TYPE" "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                                       0
  TTLL6 WILD-TYPE                                   282
D65V9, multiclass
                                       clus
vv                                      TTLL6 MUTATED TTLL6 WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                 2             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             0             282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              1              93 
     TCGA-B8-4621      TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-IZ-A6M8      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     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-B8-5158      TCGA-B8-5164      TCGA-B8-5550 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9J2      TCGA-2Z-A9J5      TCGA-2Z-A9J7      TCGA-2Z-A9J8 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9JI      TCGA-2Z-A9JK      TCGA-2Z-A9JM      TCGA-2Z-A9JN 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      TCGA-5P-A9K3 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-5P-A9KE      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-B9-4114      TCGA-B9-4115      TCGA-B9-4117 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE      TCGA-GL-7773 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A83S      TCGA-IA-A83V      TCGA-MH-A854 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-MH-A856      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-Y8-A894      TCGA-Y8-A896 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-Y8-A8RY 
"TTLL6 WILD-TYPE" 
D65V11, continuous
[1] "Remove cluster labels:" "TTLL6 MUTATED"         
clus
  TTLL6 MUTATED TTLL6 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     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-2Z-A9J3 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JN 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y      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-B9-4114      TCGA-B9-4117      TCGA-B9-A69E 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793      TCGA-G7-6795 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-IA-A40U 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-MH-A854      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"TTLL6 WILD-TYPE" "TTLL6 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TTLL6 MUTATED                                  0     0
  TTLL6 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TTLL6 MUTATED                           0     4
  TTLL6 WILD-TYPE                        83   659
D65V12, multiclass
                                  clus
vv                                 TTLL6 MUTATED TTLL6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    0              83
  WHITE                                        4             659
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                 cls
clus                0   1
  TTLL6 MUTATED     0   3
  TTLL6 WILD-TYPE  36 552
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TTLL6 MUTATED      0    3
  TTLL6 WILD-TYPE   36  552
                        clus
vv                       TTLL6 MUTATED TTLL6 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             3             552
[1] 2 2
[1] FALSE

Clustering(66) Variable = STXBP3 MUTATION ANALYSIS
D66V1, survival
                  sevent
clus2                0   1
  STXBP3 MUTATED     3   1
  STXBP3 WILD-TYPE 575 201
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               4              776 
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               1              201 
$`STXBP3 MUTATED`
TCGA-AK-3461 TCGA-B0-4841 TCGA-A4-A4ZT TCGA-B9-7268 
       72.89         6.71        16.96        22.06 

$`STXBP3 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
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-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        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-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        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-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        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-A3-3362 TCGA-A3-3367 
       48.82        52.93        45.53        88.37        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-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        94.19        46.78        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 
       37.58        38.40        82.45        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-4842 
       78.44        40.70        45.30        27.42        53.88        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        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        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        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 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W8 
       26.40        20.61         0.46         1.15        43.99        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  STXBP3 MUTATED STXBP3 WILD-TYPE 
            6.71             0.07 
  STXBP3 MUTATED STXBP3 WILD-TYPE 
           72.89           194.79 
  STXBP3 MUTATED STXBP3 WILD-TYPE 
           19.51            37.12 
[1] "6.7 - 72.9 (19.5)"  "0.1 - 194.8 (37.1)"
[1] "hr=" "1.4"
D66V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  STXBP3 MUTATED         3        1         0        1
  STXBP3 WILD-TYPE     396       88       175       92
D66V3, multiclass
           clus
vv          STXBP3 MUTATED STXBP3 WILD-TYPE
  STAGE I                3              396
  STAGE II               1               88
  STAGE III              0              175
  STAGE IV               1               92
[1] 4 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
  STXBP3 MUTATED     3   2   0   0
  STXBP3 WILD-TYPE 420 109 237  11
D66V4, multiclass
    clus
vv   STXBP3 MUTATED STXBP3 WILD-TYPE
  T1              3              420
  T2              2              109
  T3              0              237
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  STXBP3 MUTATED     1   0   0
  STXBP3 WILD-TYPE 292  40   5
D66V5, multiclass
[1] "Remove cluster labels:" "STXBP3 MUTATED"        
clus
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               1              337 
      TCGA-KL-8328       TCGA-KL-8339       TCGA-KN-8430       TCGA-A3-3358 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3450       TCGA-B0-5088       TCGA-B0-5691 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5698       TCGA-B8-4621 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4158       TCGA-BP-4160       TCGA-BP-4331       TCGA-BP-4342 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4799       TCGA-BP-4986       TCGA-BP-4988 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5191       TCGA-BP-5199 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4891       TCGA-CJ-4894 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CJ-4904       TCGA-CJ-6030       TCGA-CZ-4854       TCGA-CZ-4856 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-A4-A5Y1       TCGA-B1-A47O       TCGA-B1-A657 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5892       TCGA-BQ-7056       TCGA-IA-A83W 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-Y8-A8RZ       TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8329 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8340       TCGA-KL-8341       TCGA-KL-8342 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345       TCGA-KL-8346 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418       TCGA-KN-8419 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423       TCGA-KN-8424 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407       TCGA-KO-8408 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413       TCGA-KO-8414 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417       TCGA-A3-3313 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3362       TCGA-A3-3367       TCGA-A3-3370 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A3-3373       TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3385 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3451 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691       TCGA-B0-4693 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810       TCGA-B0-4811 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817       TCGA-B0-4823 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833       TCGA-B0-4837 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842       TCGA-B0-4843 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945       TCGA-B0-5075 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081       TCGA-B0-5083 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5092       TCGA-B0-5094 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5095       TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5106       TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5110       TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5119       TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5400       TCGA-B0-5692       TCGA-B0-5696       TCGA-B0-5697 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5699       TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5705       TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B0-5712       TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-4143       TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-4619       TCGA-B8-4620       TCGA-B8-4622       TCGA-B8-5158 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-5159       TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-5551       TCGA-B8-5553       TCGA-BP-4159       TCGA-BP-4162 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166       TCGA-BP-4169 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174       TCGA-BP-4326 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4337       TCGA-BP-4338 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4340       TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4351       TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4761       TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4787       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4960 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968       TCGA-BP-4970 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985       TCGA-BP-4989 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169       TCGA-BP-5182 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BP-5186       TCGA-BP-5198       TCGA-CJ-4638       TCGA-CJ-4639 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644       TCGA-CJ-4868 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873       TCGA-CJ-4874 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4892       TCGA-CJ-4900 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6033       TCGA-CW-5585 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4857       TCGA-CZ-4859 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-4863       TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-5984       TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-5989       TCGA-2Z-A9J1       TCGA-2Z-A9JO       TCGA-4A-A93W 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7583       TCGA-A4-7585 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A7UZ       TCGA-AL-3466 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173       TCGA-B1-5398 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B1-A655       TCGA-B1-A656       TCGA-BQ-5877       TCGA-BQ-5878 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045       TCGA-BQ-7048 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-BQ-7050       TCGA-BQ-7051       TCGA-DW-7963       TCGA-DZ-6131 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-F9-A8NY       TCGA-F9-A97G       TCGA-G7-6789       TCGA-G7-6793 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-G7-A8LD       TCGA-GL-6846 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-GL-A9DC       TCGA-IA-A40U 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-6720       TCGA-J7-8537       TCGA-J7-A8I2 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KV-A74V       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-P4-AAVL       TCGA-SX-A71R       TCGA-SX-A7SM       TCGA-SX-A7SP 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A7SS       TCGA-UN-AAZ9       TCGA-UZ-A9PM       TCGA-UZ-A9PX 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-Y8-A897 
"STXBP3 WILD-TYPE" 
D66V6, binary
                  cls
clus                 0   1
  STXBP3 MUTATED     2   1
  STXBP3 WILD-TYPE 492  80
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STXBP3 MUTATED      2    1
  STXBP3 WILD-TYPE  492   80
   clus
vv  STXBP3 MUTATED STXBP3 WILD-TYPE
  0              2              492
  1              1               80
[1] 2 2
[1] FALSE
D66V7, binary
                  cls
clus                 0   1
  STXBP3 MUTATED     1   4
  STXBP3 WILD-TYPE 257 522
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STXBP3 MUTATED      1    4
  STXBP3 WILD-TYPE  257  522
        clus
vv       STXBP3 MUTATED STXBP3 WILD-TYPE
  FEMALE              1              257
  MALE                4              522
[1] 2 2
[1] FALSE
D66V8, continuous
[1] "Remove cluster labels:" "STXBP3 MUTATED"        
clus
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-EU-5906       TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5DU 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-V9-A7HT 
"STXBP3 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  STXBP3 MUTATED                    0                                 2
  STXBP3 WILD-TYPE                 66                               434
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  STXBP3 MUTATED                                       3
  STXBP3 WILD-TYPE                                   279
D66V9, multiclass
                                       clus
vv                                      STXBP3 MUTATED STXBP3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
[1] "Remove cluster labels:" "STXBP3 MUTATED"        
clus
  STXBP3 MUTATED STXBP3 WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-5P-A9K3       TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-B9-4117       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" "STXBP3 WILD-TYPE" 
      TCGA-Y8-A8RY 
"STXBP3 WILD-TYPE" 
D66V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STXBP3 MUTATED                                  0     0
  STXBP3 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  STXBP3 MUTATED                           0     5
  STXBP3 WILD-TYPE                        83   658
D66V12, multiclass
                                  clus
vv                                 STXBP3 MUTATED STXBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         5              658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                  cls
clus                 0   1
  STXBP3 MUTATED     1   4
  STXBP3 WILD-TYPE  35 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  STXBP3 MUTATED      1    4
  STXBP3 WILD-TYPE   35  551
                        clus
vv                       STXBP3 MUTATED STXBP3 WILD-TYPE
  HISPANIC OR LATINO                  1               35
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(67) Variable = FAM20C MUTATION ANALYSIS
D67V1, survival
                  sevent
clus2                0   1
  FAM20C MUTATED     4   1
  FAM20C WILD-TYPE 574 201
  FAM20C MUTATED FAM20C WILD-TYPE 
               5              775 
  FAM20C MUTATED FAM20C WILD-TYPE 
               1              201 
$`FAM20C MUTATED`
TCGA-B1-A657 TCGA-Y8-A895 TCGA-KL-8325 TCGA-4A-A93W TCGA-Y8-A897 
       21.07        15.91        23.84         0.13        18.05 

$`FAM20C WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       21.67        27.68        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       62.83        86.37        21.60        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
      153.73       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        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-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       88.37        51.25        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       55.76        65.52        20.28       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
        5.52        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       34.36         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      105.37       123.09       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       31.66        21.57        12.00         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.30        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4337 
       64.27        54.90        53.42        27.78        62.07         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       93.99        18.48        52.24        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-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       68.38        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-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-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       26.01        39.06        18.64        18.64        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  FAM20C MUTATED FAM20C WILD-TYPE 
            0.13             0.07 
  FAM20C MUTATED FAM20C WILD-TYPE 
           23.84           194.79 
  FAM20C MUTATED FAM20C WILD-TYPE 
           18.05            37.25 
[1] "0.1 - 23.8 (18.1)"  "0.1 - 194.8 (37.2)"
[1] "hr=" "2.1"
D67V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  FAM20C MUTATED         4        1         0        0
  FAM20C WILD-TYPE     395       88       175       93
D67V3, multiclass
           clus
vv          FAM20C MUTATED FAM20C WILD-TYPE
  STAGE I                4              395
  STAGE II               1               88
  STAGE III              0              175
  STAGE IV               0               93
[1] 4 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
  FAM20C MUTATED     4   1   0   0
  FAM20C WILD-TYPE 419 110 237  11
D67V4, multiclass
    clus
vv   FAM20C MUTATED FAM20C WILD-TYPE
  T1              4              419
  T2              1              110
  T3              0              237
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM20C MUTATED     3   0   0
  FAM20C WILD-TYPE 290  40   5
D67V5, multiclass
    clus
vv   FAM20C MUTATED FAM20C WILD-TYPE
  N0              3              290
  N1              0               40
  N2              0                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"
D67V6, binary
                  cls
clus                 0   1
  FAM20C MUTATED     3   0
  FAM20C WILD-TYPE 491  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20C MUTATED      3    0
  FAM20C WILD-TYPE  491   81
   clus
vv  FAM20C MUTATED FAM20C WILD-TYPE
  0              3              491
  1              0               81
[1] 2 2
[1] FALSE
D67V7, binary
                  cls
clus                 0   1
  FAM20C MUTATED     3   2
  FAM20C WILD-TYPE 255 524
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20C MUTATED      3    2
  FAM20C WILD-TYPE  255  524
        clus
vv       FAM20C MUTATED FAM20C WILD-TYPE
  FEMALE              3              255
  MALE                2              524
[1] 2 2
[1] FALSE
D67V8, continuous
[1] "Remove cluster labels:" "FAM20C MUTATED"        
clus
  FAM20C MUTATED FAM20C WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-EU-5906       TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-4A-A93X       TCGA-4A-A93Y       TCGA-A4-7286 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310       TCGA-A4-8311 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518       TCGA-A4-8630 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-7963 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903       TCGA-F9-A7Q0 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6792       TCGA-G7-6793 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-V9-A7HT 
"FAM20C WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM20C MUTATED                    1                                 0
  FAM20C WILD-TYPE                 65                               436
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM20C MUTATED                                       4
  FAM20C WILD-TYPE                                   278
D67V9, multiclass
                                       clus
vv                                      FAM20C MUTATED FAM20C WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  0              436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
[1] "Remove cluster labels:" "FAM20C MUTATED"        
clus
  FAM20C MUTATED FAM20C WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93Y       TCGA-5P-A9K3 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D       TCGA-A4-A57E 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115       TCGA-B9-4117 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963       TCGA-F9-A97G 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-6792       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-Y8-A8RY 
"FAM20C WILD-TYPE" 
D67V11, continuous
[1] "Remove cluster labels:" "FAM20C MUTATED"        
clus
  FAM20C MUTATED FAM20C WILD-TYPE 
               1               66 
      TCGA-2Z-A9JD       TCGA-DW-5561       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-AK-3445       TCGA-AK-3451       TCGA-B8-5158       TCGA-B8-5550 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-2Z-A9J3       TCGA-2Z-A9J7       TCGA-2Z-A9J8       TCGA-2Z-A9JI 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93Y       TCGA-A4-A48D 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472       TCGA-AL-7173 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4117       TCGA-B9-A69E 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-DW-7963       TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-G7-7501       TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-GL-7773       TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-IA-A40U 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-MH-A854       TCGA-MH-A856       TCGA-P4-A5E6       TCGA-Q2-A5QZ 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-WN-AB4C       TCGA-Y8-A894 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
      TCGA-Y8-A896       TCGA-Y8-A8RY 
"FAM20C WILD-TYPE" "FAM20C WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM20C MUTATED                                  0     0
  FAM20C WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM20C MUTATED                           0     5
  FAM20C WILD-TYPE                        83   658
D67V12, multiclass
                                  clus
vv                                 FAM20C MUTATED FAM20C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     0               83
  WHITE                                         5              658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                  cls
clus                 0   1
  FAM20C MUTATED     0   4
  FAM20C WILD-TYPE  36 551
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM20C MUTATED      0    4
  FAM20C WILD-TYPE   36  551
                        clus
vv                       FAM20C MUTATED FAM20C WILD-TYPE
  HISPANIC OR LATINO                  0               36
  NOT HISPANIC OR LATINO              4              551
[1] 2 2
[1] FALSE

Clustering(68) Variable = CCBL2 MUTATION ANALYSIS
D68V1, survival
                 sevent
clus2               0   1
  CCBL2 MUTATED     2   1
  CCBL2 WILD-TYPE 576 201
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              3             777 
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              1             201 
$`CCBL2 MUTATED`
TCGA-Y8-A898 TCGA-B0-4818 TCGA-MH-A854 
       15.62        16.77        17.62 

$`CCBL2 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       27.02        31.79        44.55        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       27.65       108.56       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        0.59       107.54         5.46        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       11.67        66.28        56.84        23.90        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W 
       12.13        29.26        19.73        17.75        12.49        35.38 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A8RZ 
       41.33        62.83        86.37        21.60        15.91         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4819 
       46.59         0.59         5.52        45.07        33.50         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 
       18.12         3.91         6.77         4.18         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         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-A6HP 
       16.96         8.48        16.31        15.75         8.28        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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         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-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
       99.12        92.58        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  CCBL2 MUTATED CCBL2 WILD-TYPE 
          15.62            0.07 
  CCBL2 MUTATED CCBL2 WILD-TYPE 
          17.62          194.79 
  CCBL2 MUTATED CCBL2 WILD-TYPE 
          16.77           37.22 
[1] "15.6 - 17.6 (16.8)" "0.1 - 194.8 (37.2)"
[1] "hr=" "3.4"
D68V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CCBL2 MUTATED         2        1         0        0
  CCBL2 WILD-TYPE     397       88       175       93
D68V3, multiclass
           clus
vv          CCBL2 MUTATED CCBL2 WILD-TYPE
  STAGE I               2             397
  STAGE II              1              88
  STAGE III             0             175
  STAGE IV              0              93
[1] 4 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
  CCBL2 MUTATED     2   1   0   0
  CCBL2 WILD-TYPE 421 110 237  11
D68V4, multiclass
    clus
vv   CCBL2 MUTATED CCBL2 WILD-TYPE
  T1             2             421
  T2             1             110
  T3             0             237
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CCBL2 MUTATED     0   0   0
  CCBL2 WILD-TYPE 293  40   5
D68V5, multiclass
D68V6, binary
                 cls
clus                0   1
  CCBL2 MUTATED     1   0
  CCBL2 WILD-TYPE 493  81
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCBL2 MUTATED      1    0
  CCBL2 WILD-TYPE  493   81
   clus
vv  CCBL2 MUTATED CCBL2 WILD-TYPE
  0             1             493
  1             0              81
[1] 2 2
[1] FALSE
D68V7, binary
                 cls
clus                0   1
  CCBL2 MUTATED     2   1
  CCBL2 WILD-TYPE 256 525
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCBL2 MUTATED      2    1
  CCBL2 WILD-TYPE  256  525
        clus
vv       CCBL2 MUTATED CCBL2 WILD-TYPE
  FEMALE             2             256
  MALE               1             525
[1] 2 2
[1] FALSE
D68V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CCBL2 MUTATED                    0                                 1
  CCBL2 WILD-TYPE                 66                               435
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CCBL2 MUTATED                                       2
  CCBL2 WILD-TYPE                                   280
D68V9, multiclass
                                       clus
vv                                      CCBL2 MUTATED CCBL2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 1             435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
[1] "Remove cluster labels:" "CCBL2 MUTATED"         
clus
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              1              93 
     TCGA-B8-4621      TCGA-2Z-A9JD      TCGA-2Z-A9JQ      TCGA-5P-A9JU 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7838 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-GL-A59T      TCGA-IZ-A6M8      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-AK-3445 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-AK-3451      TCGA-B8-4146      TCGA-B8-5158      TCGA-B8-5164 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-B8-5550      TCGA-2Z-A9J2      TCGA-2Z-A9J5      TCGA-2Z-A9J7 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-2Z-A9J8      TCGA-2Z-A9JI      TCGA-2Z-A9JK      TCGA-2Z-A9JM 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-5P-A9K3      TCGA-5P-A9KE      TCGA-A4-8310      TCGA-A4-A48D 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4115 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-7963 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-F9-A97G      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD      TCGA-G7-A8LE 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI      TCGA-HE-A5NJ 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IA-A83S      TCGA-IA-A83V 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-MH-A856      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-Y8-A894      TCGA-Y8-A896 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-Y8-A8RY 
"CCBL2 WILD-TYPE" 
D68V11, continuous
[1] "Remove cluster labels:" "CCBL2 MUTATED"         
clus
  CCBL2 MUTATED CCBL2 WILD-TYPE 
              1              66 
     TCGA-2Z-A9JD      TCGA-DW-5561      TCGA-PJ-A5Z9      TCGA-PJ-A8JU 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A71W      TCGA-UZ-A9PO      TCGA-UZ-A9PR      TCGA-Y8-A8RZ 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-AK-3445      TCGA-AK-3451      TCGA-B8-5158      TCGA-B8-5550 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-2Z-A9J3      TCGA-2Z-A9J7      TCGA-2Z-A9J8      TCGA-2Z-A9JI 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-2Z-A9JN      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93Y 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4114      TCGA-B9-4117 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-7963      TCGA-F9-A97G      TCGA-G7-6793 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LB      TCGA-G7-A8LD 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-G7-A8LE      TCGA-GL-7773      TCGA-GL-A9DD      TCGA-HE-A5NI 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-MH-A856      TCGA-P4-A5E6      TCGA-Q2-A5QZ 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A71S      TCGA-SX-A71U      TCGA-SX-A7SL      TCGA-SX-A7SM 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-SX-A7SR      TCGA-SX-A7SS      TCGA-UZ-A9PM      TCGA-UZ-A9PS 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-UZ-A9PX      TCGA-WN-A9G9      TCGA-WN-AB4C      TCGA-Y8-A894 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
     TCGA-Y8-A896      TCGA-Y8-A8RY 
"CCBL2 WILD-TYPE" "CCBL2 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCBL2 MUTATED                                  0     0
  CCBL2 WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CCBL2 MUTATED                           1     2
  CCBL2 WILD-TYPE                        82   661
D68V12, multiclass
                                  clus
vv                                 CCBL2 MUTATED CCBL2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    1              82
  WHITE                                        2             661
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                 cls
clus                0   1
  CCBL2 MUTATED     0   3
  CCBL2 WILD-TYPE  36 552
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CCBL2 MUTATED      0    3
  CCBL2 WILD-TYPE   36  552
                        clus
vv                       CCBL2 MUTATED CCBL2 WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             3             552
[1] 2 2
[1] FALSE

Clustering(69) Variable = B3GNT6 MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  B3GNT6 MUTATED     2   1
  B3GNT6 WILD-TYPE 576 201
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               3              777 
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               1              201 
$`B3GNT6 MUTATED`
TCGA-BP-5168 TCGA-G7-6792 TCGA-P4-A5ED 
       48.10        90.90        92.58 

$`B3GNT6 WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       43.96        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 
      111.02        94.72        32.61        80.68        74.17        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       41.62        27.62        35.90        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       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-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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 
       52.93        45.53        88.37        51.25        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
       53.29        43.20        55.76        65.52        20.28       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       94.19        46.78        78.64        94.29        83.21        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 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-B0-5092 
       11.24        11.90        34.36         7.30        25.32        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-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       73.84       149.16       105.37       123.09       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       31.96        21.30        31.66        21.57        12.00         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
        0.53        34.39        14.30        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       62.07         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       61.97        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66         1.35        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 
       69.21        58.75        14.66        63.39       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-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-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE 
       62.63        18.12         3.91         6.77         4.18         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       15.48        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
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-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        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-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R 
        6.61        99.12        16.01        50.60        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
           48.10             0.07 
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
           92.58           194.79 
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
           90.90            36.95 
[1] "48.1 - 92.6 (90.9)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.4"
D69V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  B3GNT6 MUTATED         3        0         0        0
  B3GNT6 WILD-TYPE     396       89       175       93
D69V3, multiclass
           clus
vv          B3GNT6 MUTATED B3GNT6 WILD-TYPE
  STAGE I                3              396
  STAGE II               0               89
  STAGE III              0              175
  STAGE IV               0               93
[1] 4 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
  B3GNT6 MUTATED     3   0   0   0
  B3GNT6 WILD-TYPE 420 111 237  11
D69V4, multiclass
    clus
vv   B3GNT6 MUTATED B3GNT6 WILD-TYPE
  T1              3              420
  T2              0              111
  T3              0              237
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  B3GNT6 MUTATED     0   0   0
  B3GNT6 WILD-TYPE 293  40   5
D69V5, multiclass
D69V6, binary
                  cls
clus                 0   1
  B3GNT6 MUTATED     1   0
  B3GNT6 WILD-TYPE 493  81
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT6 MUTATED      1    0
  B3GNT6 WILD-TYPE  493   81
   clus
vv  B3GNT6 MUTATED B3GNT6 WILD-TYPE
  0              1              493
  1              0               81
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  B3GNT6 MUTATED     0   3
  B3GNT6 WILD-TYPE 258 523
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT6 MUTATED      0    3
  B3GNT6 WILD-TYPE  258  523
        clus
vv       B3GNT6 MUTATED B3GNT6 WILD-TYPE
  FEMALE              0              258
  MALE                3              523
[1] 2 2
[1] FALSE
D69V8, continuous
[1] "Remove cluster labels:" "B3GNT6 MUTATED"        
clus
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               1              125 
      TCGA-KM-8439       TCGA-KM-8441       TCGA-KM-8442       TCGA-KO-8411 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4862       TCGA-DV-5565 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-2Z-A9JL       TCGA-2Z-A9JT 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-5P-A9JU       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-DW-7836       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-SX-A71W 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A7SO       TCGA-UZ-A9PZ       TCGA-KM-8438       TCGA-KM-8440 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477       TCGA-KM-8639 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8434       TCGA-KO-8413       TCGA-AK-3428 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4622 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B8-5158       TCGA-CJ-6028       TCGA-CZ-4858       TCGA-CZ-4861 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5458       TCGA-CZ-5465 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-EU-5904       TCGA-EU-5905 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-EU-5906       TCGA-EU-5907       TCGA-2Z-A9JE       TCGA-2Z-A9JK 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-4A-A93W       TCGA-4A-A93X       TCGA-4A-A93Y 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8098       TCGA-A4-8310 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8517       TCGA-A4-8518 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-A4-8630       TCGA-A4-A48D       TCGA-A4-A4ZT       TCGA-A4-A57E 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902       TCGA-EV-5903 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-F9-A7Q0       TCGA-G7-6789       TCGA-G7-6790       TCGA-G7-6793 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-G7-7502       TCGA-G7-A4TM       TCGA-G7-A8LB       TCGA-G7-A8LC 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-IA-A40U       TCGA-IA-A40X 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-IA-A40Y       TCGA-J7-8537       TCGA-Q2-A5QZ       TCGA-SX-A71R 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A71V       TCGA-SX-A7SL 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A7SM       TCGA-SX-A7SN       TCGA-SX-A7SP       TCGA-SX-A7SQ 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-SX-A7SU       TCGA-UZ-A9PL 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-V9-A7HT 
"B3GNT6 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  B3GNT6 MUTATED                    0                                 1
  B3GNT6 WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  B3GNT6 MUTATED                                       2
  B3GNT6 WILD-TYPE                                   280
D69V9, multiclass
                                       clus
vv                                      B3GNT6 MUTATED B3GNT6 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
[1] "Remove cluster labels:" "B3GNT6 MUTATED"        
clus
  B3GNT6 MUTATED B3GNT6 WILD-TYPE 
               1               93 
      TCGA-B8-4621       TCGA-2Z-A9JD       TCGA-2Z-A9JQ       TCGA-5P-A9JU 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7838 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-GL-A59T       TCGA-IZ-A6M8       TCGA-PJ-A5Z9       TCGA-PJ-A8JU 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A71W       TCGA-UZ-A9PO       TCGA-UZ-A9PR       TCGA-Y8-A8RZ 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-AK-3445 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-AK-3451       TCGA-B8-4146       TCGA-B8-5158       TCGA-B8-5164 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B8-5550       TCGA-2Z-A9J2       TCGA-2Z-A9J5       TCGA-2Z-A9J7 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-2Z-A9J8       TCGA-2Z-A9JI       TCGA-2Z-A9JK       TCGA-2Z-A9JM 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-2Z-A9JN       TCGA-2Z-A9JO       TCGA-4A-A93W       TCGA-4A-A93Y 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-5P-A9K3       TCGA-5P-A9KE       TCGA-A4-8310       TCGA-A4-A48D 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4114       TCGA-B9-4115 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-B9-4117       TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-7963 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-F9-A97G       TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-G7-A8LB       TCGA-G7-A8LD       TCGA-G7-A8LE       TCGA-GL-7773 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-GL-A9DD       TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A83S       TCGA-IA-A83V       TCGA-MH-A854 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-MH-A856       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-Q2-A5QZ 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A71S       TCGA-SX-A71U       TCGA-SX-A7SL       TCGA-SX-A7SM 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-SX-A7SR       TCGA-SX-A7SS       TCGA-UZ-A9PM       TCGA-UZ-A9PS 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-UZ-A9PX       TCGA-WN-A9G9       TCGA-Y8-A894       TCGA-Y8-A896 
"B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" "B3GNT6 WILD-TYPE" 
      TCGA-Y8-A8RY 
"B3GNT6 WILD-TYPE" 
D69V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  B3GNT6 MUTATED                                  0     0
  B3GNT6 WILD-TYPE                                2    14
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  B3GNT6 MUTATED                           1     2
  B3GNT6 WILD-TYPE                        82   661
D69V12, multiclass
                                  clus
vv                                 B3GNT6 MUTATED B3GNT6 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               14
  BLACK OR AFRICAN AMERICAN                     1               82
  WHITE                                         2              661
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                  cls
clus                 0   1
  B3GNT6 MUTATED     1   1
  B3GNT6 WILD-TYPE  35 554
[1] "tbl2"
                  cls
clus               [,1] [,2]
  B3GNT6 MUTATED      1    1
  B3GNT6 WILD-TYPE   35  554
                        clus
vv                       B3GNT6 MUTATED B3GNT6 WILD-TYPE
  HISPANIC OR LATINO                  1               35
  NOT HISPANIC OR LATINO              1              554
[1] 2 2
[1] FALSE

Clustering(70) Variable = HNF1B MUTATION ANALYSIS
D70V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     2   2
  HNF1B WILD-TYPE 576 200
  HNF1B MUTATED HNF1B WILD-TYPE 
              4             776 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             200 
$`HNF1B MUTATED`
TCGA-B0-5694 TCGA-KN-8431 TCGA-CW-5580 TCGA-2Z-A9JP 
       15.78        19.33        64.57        29.36 

$`HNF1B WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3358 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 
       42.97       109.91        58.49        28.73        22.45        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 
       43.96        52.21        18.51       112.80       133.94        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-BP-4158 
      119.38       126.05        24.82        25.91         1.18       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4760 TCGA-BP-4762 
       94.72        32.61        80.68        74.17        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       66.28        56.84        23.90        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-SX-A71W TCGA-SX-A7SO 
       29.26        19.73        17.75        12.49        35.38        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.99        52.27        87.12         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-8413 
      103.40        92.71        16.67       104.55       103.10        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-A3-3362 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       45.53        88.37        51.25        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       43.20        55.76        65.52        20.28       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       46.78        78.64        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89        12.13        40.70         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.90        34.36         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 
       38.43        48.82        46.39        56.98        42.41       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      149.16       105.37       123.09       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        31.66        21.57        12.00         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       34.39        14.30        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        52.24        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-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        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 
       67.00        53.42        62.66       119.64         7.36        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39       107.41        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-EU-5904 
       65.65        12.26        14.63        22.78        62.63        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         6.77         4.18         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        15.48        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         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-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
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-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        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-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         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        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        16.01        50.60        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  HNF1B MUTATED HNF1B WILD-TYPE 
          15.78            0.07 
  HNF1B MUTATED HNF1B WILD-TYPE 
          64.57          194.79 
  HNF1B MUTATED HNF1B WILD-TYPE 
         24.345          37.120 
[1] "15.8 - 64.6 (24.3)" "0.1 - 194.8 (37.1)"
[1] "hr=" "2.6"
D70V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HNF1B MUTATED         1        1         1        1
  HNF1B WILD-TYPE     398       88       174       92
D70V3, multiclass
           clus
vv          HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I               1             398
  STAGE II              1              88
  STAGE III             1             174
  STAGE IV              1              92
[1] 4 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
  HNF1B MUTATED     1   1   2   0
  HNF1B WILD-TYPE 422 110 235  11
D70V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             1             422
  T2             1             110
  T3             2             235
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HNF1B MUTATED     1   0   0
  HNF1B WILD-TYPE 292  40   5
D70V5, multiclass
[1] "Remove cluster labels:" "HNF1B MUTATED"         
clus
  HNF1B MUTATED HNF1B WILD-TYPE 
              1             337 
     TCGA-KL-8328      TCGA-KL-8339      TCGA-KN-8430      TCGA-A3-3358 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3450      TCGA-B0-5088      TCGA-B0-5691 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5695      TCGA-B0-5698      TCGA-B8-4621      TCGA-BP-4158 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4160      TCGA-BP-4331      TCGA-BP-4342      TCGA-BP-4795 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4799      TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4995 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5191      TCGA-BP-5199      TCGA-BP-5201 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4636      TCGA-CJ-4891      TCGA-CJ-4894      TCGA-CJ-4904 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-6030      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-5P-A9JU 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-B1-A47O      TCGA-B1-A657      TCGA-BQ-5888 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-7056      TCGA-IA-A83W      TCGA-Y8-A8RZ 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8329      TCGA-KL-8330 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333      TCGA-KL-8334 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337      TCGA-KL-8338 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342      TCGA-KL-8343 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346      TCGA-KM-8438 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KM-8443      TCGA-KN-8418      TCGA-KN-8419      TCGA-KN-8421 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8422      TCGA-KN-8423      TCGA-KN-8424      TCGA-KN-8425 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429      TCGA-KO-8405 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8410      TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8416      TCGA-KO-8417      TCGA-A3-3313      TCGA-A3-3317 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3331      TCGA-A3-3347      TCGA-A3-3349      TCGA-A3-3357 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3362      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3385      TCGA-A3-3387 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429      TCGA-AK-3430 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3436      TCGA-AK-3443      TCGA-AK-3451      TCGA-AK-3456 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4690      TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4710      TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4816      TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4827      TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4839      TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5085      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5699 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4620      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4159      TCGA-BP-4162      TCGA-BP-4163 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4330      TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4960      TCGA-BP-4964 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4989      TCGA-BP-5007 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5198      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4890      TCGA-CJ-4892      TCGA-CJ-4900      TCGA-CJ-4918 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CW-6087      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-2Z-A9J1      TCGA-2Z-A9JO      TCGA-4A-A93W      TCGA-4A-A93X 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-4A-A93Y      TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A7UZ      TCGA-AL-3466      TCGA-AL-3472 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B1-A656      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-DW-7963      TCGA-DZ-6131 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-F9-A8NY      TCGA-F9-A97G      TCGA-G7-6789      TCGA-G7-6793 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-G7-A8LD      TCGA-GL-6846 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-GL-A9DC      TCGA-IA-A40U 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-IA-A40Y      TCGA-J7-6720      TCGA-J7-8537      TCGA-J7-A8I2 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KV-A74V      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-P4-AAVL      TCGA-SX-A71R      TCGA-SX-A7SM      TCGA-SX-A7SP 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-SX-A7SS      TCGA-UN-AAZ9      TCGA-UZ-A9PM      TCGA-UZ-A9PX 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-Y8-A897 
"HNF1B WILD-TYPE" 
D70V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     1   1
  HNF1B WILD-TYPE 493  80
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      1    1
  HNF1B WILD-TYPE  493   80
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             1             493
  1             1              80
[1] 2 2
[1] FALSE
D70V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     2   2
  HNF1B WILD-TYPE 256 524
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      2    2
  HNF1B WILD-TYPE  256  524
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             2             256
  MALE               2             524
[1] 2 2
[1] FALSE
D70V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  HNF1B MUTATED                    1                                 2
  HNF1B WILD-TYPE                 65                               434
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  HNF1B MUTATED                                       1
  HNF1B WILD-TYPE                                   281
D70V9, multiclass
                                       clus
vv                                      HNF1B MUTATED HNF1B WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 2             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
D70V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1B MUTATED                                  0     0
  HNF1B WILD-TYPE                                2    14
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1B MUTATED                           0     3
  HNF1B WILD-TYPE                        83   660
D70V12, multiclass
                                  clus
vv                                 HNF1B MUTATED HNF1B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              14
  BLACK OR AFRICAN AMERICAN                    0              83
  WHITE                                        3             660
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   3
  HNF1B WILD-TYPE  36 552
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    3
  HNF1B WILD-TYPE   36  552
                        clus
vv                       HNF1B MUTATED HNF1B WILD-TYPE
  HISPANIC OR LATINO                 0              36
  NOT HISPANIC OR LATINO             3             552
[1] 2 2
[1] FALSE
