[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/15081103/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/15639742/transformed.cor.cli.txt"

nPatients in clinical file=914, in cluster file=742, common to both=668
[1] "Reduce the number of clustering variables from 75 to 73."
[1]  73 668
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            38            630 
  TP53 MUTATED TP53 WILD-TYPE 
            38            630 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            146             522 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            146             522 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            28            640 
  PTEN MUTATED PTEN WILD-TYPE 
            28            640 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            49            619 
  BAP1 MUTATED BAP1 WILD-TYPE 
            49            619 
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             58             610 
  SETD2 MUTATED SETD2 WILD-TYPE 
             58             610 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             30             638 
  KDM5C MUTATED KDM5C WILD-TYPE 
             30             638 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
            15            653 
  NEFH MUTATED NEFH WILD-TYPE 
            15            653 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          174           494 
  VHL MUTATED VHL WILD-TYPE 
          174           494 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
           16           652 
  NF2 MUTATED NF2 WILD-TYPE 
           16           652 
[1] "HNRNPM MUTATION ANALYSIS"
[1] 3
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              656 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              656 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
           19           649 
  MET MUTATED MET WILD-TYPE 
           19           649 
[1] "MUC5B MUTATION ANALYSIS"
[1] 3
  MUC5B MUTATED MUC5B WILD-TYPE 
             30             638 
  MUC5B MUTATED MUC5B WILD-TYPE 
             30             638 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             11             657 
  KDM6A MUTATED KDM6A WILD-TYPE 
             11             657 
[1] "TDG MUTATION ANALYSIS"
[1] 3
  TDG MUTATED TDG WILD-TYPE 
            5           663 
  TDG MUTATED TDG WILD-TYPE 
            5           663 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              658 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              658 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           16           652 
  ATM MUTATED ATM WILD-TYPE 
           16           652 
[1] "ZNF814 MUTATION ANALYSIS"
[1] 3
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              655 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              655 
[1] "DNMT3A MUTATION ANALYSIS"
[1] 3
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              658 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              658 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              9             659 
  CDK12 MUTATED CDK12 WILD-TYPE 
              9             659 
[1] "CSGALNACT2 MUTATION ANALYSIS"
[1] 3
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   8                  660 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   8                  660 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              654 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              654 
[1] "KIAA1751 MUTATION ANALYSIS"
[1] 3
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 8                660 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 8                660 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            32            636 
  MTOR MUTATED MTOR WILD-TYPE 
            32            636 
[1] "RIMBP3 MUTATION ANALYSIS"
[1] 3
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              663 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              663 
[1] "ZNF598 MUTATION ANALYSIS"
[1] 3
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              11              657 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              11              657 
[1] "GPR50 MUTATION ANALYSIS"
[1] 3
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             663 
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             663 
[1] "CCDC120 MUTATION ANALYSIS"
[1] 3
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               664 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               664 
[1] "SLC6A14 MUTATION ANALYSIS"
[1] 3
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               663 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               663 
[1] "CYP4F11 MUTATION ANALYSIS"
[1] 3
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               663 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               663 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             654 
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             654 
[1] "SKI MUTATION ANALYSIS"
[1] 3
  SKI MUTATED SKI WILD-TYPE 
            9           659 
  SKI MUTATED SKI WILD-TYPE 
            9           659 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              649 
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              649 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             7            661 
  EGFR MUTATED EGFR WILD-TYPE 
             7            661 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             660 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             660 
[1] "GUSB MUTATION ANALYSIS"
[1] 3
  GUSB MUTATED GUSB WILD-TYPE 
             4            664 
  GUSB MUTATED GUSB WILD-TYPE 
             4            664 
[1] "MED16 MUTATION ANALYSIS"
[1] 3
  MED16 MUTATED MED16 WILD-TYPE 
              4             664 
  MED16 MUTATED MED16 WILD-TYPE 
              4             664 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              8             660 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              8             660 
[1] "AHNAK2 MUTATION ANALYSIS"
[1] 3
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              635 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              635 
[1] "RLIM MUTATION ANALYSIS"
[1] 3
  RLIM MUTATED RLIM WILD-TYPE 
             9            659 
  RLIM MUTATED RLIM WILD-TYPE 
             9            659 
[1] "SLC23A1 MUTATION ANALYSIS"
[1] 3
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                7               661 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                7               661 
[1] "STAM MUTATION ANALYSIS"
[1] 3
  STAM MUTATED STAM WILD-TYPE 
             6            662 
  STAM MUTATED STAM WILD-TYPE 
             6            662 
[1] "RHEB MUTATION ANALYSIS"
[1] 3
  RHEB MUTATED RHEB WILD-TYPE 
             4            664 
  RHEB MUTATED RHEB WILD-TYPE 
             4            664 
[1] "SLC4A8 MUTATION ANALYSIS"
[1] 3
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               6              662 
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               6              662 
[1] "RUFY3 MUTATION ANALYSIS"
[1] 3
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              7             661 
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              7             661 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             6            662 
  PCK1 MUTATED PCK1 WILD-TYPE 
             6            662 
[1] "TXNIP MUTATION ANALYSIS"
[1] 3
  TXNIP MUTATED TXNIP WILD-TYPE 
              8             660 
  TXNIP MUTATED TXNIP WILD-TYPE 
              8             660 
[1] "RNF128 MUTATION ANALYSIS"
[1] 3
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              663 
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              663 
[1] "ZFYVE26 MUTATION ANALYSIS"
[1] 3
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                9               659 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                9               659 
[1] "FAM160B2 MUTATION ANALYSIS"
[1] 3
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                664 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                664 
[1] "FAM47A MUTATION ANALYSIS"
[1] 3
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              662 
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              662 
[1] "ATP1A1 MUTATION ANALYSIS"
[1] 3
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
              10              658 
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
              10              658 
[1] "SH3BP2 MUTATION ANALYSIS"
[1] 3
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              664 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              664 
[1] "FAM200A MUTATION ANALYSIS"
[1] 3
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               663 
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               663 
[1] "RTL1 MUTATION ANALYSIS"
[1] 3
  RTL1 MUTATED RTL1 WILD-TYPE 
             7            661 
  RTL1 MUTATED RTL1 WILD-TYPE 
             7            661 
[1] "NASP MUTATION ANALYSIS"
[1] 3
  NASP MUTATED NASP WILD-TYPE 
             4            664 
  NASP MUTATED NASP WILD-TYPE 
             4            664 
[1] "RPL7A MUTATION ANALYSIS"
[1] 3
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             665 
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             665 
[1] "UIMC1 MUTATION ANALYSIS"
[1] 3
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              5             663 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              5             663 
[1] "TCEB1 MUTATION ANALYSIS"
[1] 3
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              3             665 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              3             665 
[1] "SFMBT1 MUTATION ANALYSIS"
[1] 3
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
               3              665 
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
               3              665 
[1] "SLC16A1 MUTATION ANALYSIS"
[1] 3
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               665 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               665 
[1] "PAM MUTATION ANALYSIS"
[1] 3
  PAM MUTATED PAM WILD-TYPE 
            4           664 
  PAM MUTATED PAM WILD-TYPE 
            4           664 
[1] "TMCO3 MUTATION ANALYSIS"
[1] 3
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             661 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             661 
[1] "CCDC82 MUTATION ANALYSIS"
[1] 3
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               6              662 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               6              662 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              8             660 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              8             660 
[1] "HNF1B MUTATION ANALYSIS"
[1] 3
  HNF1B MUTATED HNF1B WILD-TYPE 
              3             665 
  HNF1B MUTATED HNF1B WILD-TYPE 
              3             665 
[1] "OR2L8 MUTATION ANALYSIS"
[1] 3
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              7             661 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              7             661 
[1] "IDUA MUTATION ANALYSIS"
[1] 3
  IDUA MUTATED IDUA WILD-TYPE 
             5            663 
  IDUA MUTATED IDUA WILD-TYPE 
             5            663 
[1] "ZC3H18 MUTATION ANALYSIS"
[1] 3
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               6              662 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               6              662 
[1] "GAPDHS MUTATION ANALYSIS"
[1] 3
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              663 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              663 
[1] "GPR137 MUTATION ANALYSIS"
[1] 3
  GPR137 MUTATED GPR137 WILD-TYPE 
               4              664 
  GPR137 MUTATED GPR137 WILD-TYPE 
               4              664 
[1] "GFM1 MUTATION ANALYSIS"
[1] 3
  GFM1 MUTATED GFM1 WILD-TYPE 
             3            665 
  GFM1 MUTATED GFM1 WILD-TYPE 
             3            665 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            22            646 
  FAT1 MUTATED FAT1 WILD-TYPE 
            22            646 
[1] "RRP12 MUTATION ANALYSIS"
[1] 3
  RRP12 MUTATED RRP12 WILD-TYPE 
              9             659 
  RRP12 MUTATED RRP12 WILD-TYPE 
              9             659 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 668 columns.

[1] "Batch" "22"   
[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=165,	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=463,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'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 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=53,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "667"  
freq.contrast "667"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=32,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 668 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"                "NEOPLASM_DISEASESTAGE"        
 [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
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
340  97 221  10 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
340  97 221  10 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
340  97 221  10 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
340  97 221  10 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
272  36   6 
[1] "table(vv)"
vv
 N0  N1  N2 
272  36   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
272  36   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
272  36   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=25, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=22, 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    24  14
  TP53 WILD-TYPE 462 161
  TP53 MUTATED TP53 WILD-TYPE 
            38            623 
  TP53 MUTATED TP53 WILD-TYPE 
            14            161 
$`TP53 MUTATED`
TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
      141.73        90.48        92.55        30.25        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8341 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8428 
       28.11        24.79       129.37        25.91        65.19        52.27 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 
       19.33        11.21        59.08        42.35        76.90        10.68 
TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-AK-3440 TCGA-B0-4703 
       16.67        86.10        77.85        61.58        57.37         5.98 
TCGA-B0-4710 TCGA-B0-5098 TCGA-B0-5117 TCGA-BP-4176 TCGA-BP-4770 TCGA-BP-4798 
        3.16        52.08        17.59        64.27        10.82        10.98 
TCGA-CJ-5677 TCGA-CZ-4858 TCGA-CZ-4865 TCGA-CZ-5463 TCGA-A4-A57E TCGA-B1-A655 
       25.71        69.21         5.46        21.76         8.48        16.77 
TCGA-B3-4104 TCGA-BQ-5881 
       34.49        47.80 

$`TP53 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
       38.07        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 
       98.96        84.89        98.33        96.95        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8426 
       31.33        23.47        87.91        25.48       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8405 
        0.99        87.12         2.50       115.00       100.87        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 
       79.04        92.71        80.38        87.78       103.27        57.17 
TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       63.95        39.16        49.08        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 
       37.38        48.82        52.93        45.53        88.37        42.97 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       43.20        55.76        18.64        28.31        65.52        20.28 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
      109.91        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       68.61        67.20        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 
        2.53         3.48        19.00        65.10         2.14        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       61.78        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        36.39        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
       18.77        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        60.59        63.39        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        47.01        10.85        10.22        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        24.56         3.55         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  TP53 MUTATED TP53 WILD-TYPE 
          3.16           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
        141.73         194.79 
  TP53 MUTATED TP53 WILD-TYPE 
         38.42          34.19 
[1] "3.2 - 141.7 (38.4)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED        12       11         7        8
  TP53 WILD-TYPE     315       68       158       78
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I             12            315
  STAGE II            11             68
  STAGE III            7            158
  STAGE IV             8             78
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  TP53 MUTATED    12  12  12   2
  TP53 WILD-TYPE 328  85 209   8
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           12            328
  T2           12             85
  T3           12            209
  T4            2              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  TP53 MUTATED    17   2   2
  TP53 WILD-TYPE 255  34   4
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           17            255
  N1            2             34
  N2            2              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                cls
clus               0   1
  TP53 MUTATED    22   5
  TP53 WILD-TYPE 446  73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     22    5
  TP53 WILD-TYPE  446   73
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           22            446
  1            5             73
[1] 2 2
[1] FALSE
D1V7, binary
                cls
clus               0   1
  TP53 MUTATED    15  23
  TP53 WILD-TYPE 214 416
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     15   23
  TP53 WILD-TYPE  214  416
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           15            214
  MALE             23            416
[1] 2 2
[1] FALSE
D1V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TP53 MUTATED                   22                                12
  TP53 WILD-TYPE                 44                               429
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TP53 MUTATED                                       4
  TP53 WILD-TYPE                                   157
D1V9, multiclass
                                       clus
vv                                      TP53 MUTATED TP53 WILD-TYPE
  KIDNEY CHROMOPHOBE                              22             44
  KIDNEY CLEAR CELL RENAL CARCINOMA               12            429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            4            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  0     2
  TP53 WILD-TYPE                                2     9
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                           2    33
  TP53 WILD-TYPE                        63   536
D1V12, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       2              9
  BLACK OR AFRICAN AMERICAN                   2             63
  WHITE                                      33            536
[1] 4 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  22
  TP53 WILD-TYPE  31 419
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   22
  TP53 WILD-TYPE   31  419
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1             31
  NOT HISPANIC OR LATINO           22            419
[1] 2 2
[1] FALSE

Clustering(2) Variable = PBRM1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED   100  45
  PBRM1 WILD-TYPE 386 130
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            145             516 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             45             130 
$`PBRM1 MUTATED`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       39.16        49.08        48.59        36.36        37.38        48.82 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3431 
       51.25        74.63        53.29        20.28       109.91        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3458 TCGA-AK-3460 TCGA-B0-4706 
       68.61        67.20        42.08        38.40        31.27         2.14 
TCGA-B0-4718 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4822 TCGA-B0-4824 
       20.25        52.21        45.07        16.77        36.53        54.48 
TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.09        56.68        65.29        26.07         2.27        36.85 
TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5110 
       25.32        10.95         2.24        90.48        30.48        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5693 
       11.80        26.20        21.60        16.21        21.44       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 
       15.78        46.68        56.78        84.92        90.12        39.55 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-4099 
      120.59        47.97        96.36        89.49        61.32        12.30 
TCGA-B2-4101 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4148 
       21.30         9.57         0.23         4.64         0.23        27.16 
TCGA-B8-4154 TCGA-B8-5158 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4176 
       24.66        20.91       111.02        85.51        32.61        64.27 
TCGA-BP-4329 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4759 TCGA-BP-4774 TCGA-BP-4801 
       27.78         0.07        52.24        77.98        61.97        36.95 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4981 
        6.71        71.41        61.22        45.50        47.11        36.07 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4993 
       33.34        31.30        36.95        27.22         3.88         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 
       45.07        41.62        48.10         6.35        79.30        74.40 
TCGA-BP-5181 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5198 
       49.15        37.25        22.78        13.35        27.02        19.82 
TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 
       34.95        59.84        46.55        11.05        79.66        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4903 TCGA-CJ-4905 
       77.36        57.83        30.64        51.52        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5676 
       50.33        54.48        38.56         4.57        18.81        84.66 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6030 TCGA-CJ-6033 
       18.87        22.32        61.91        73.35        75.58         7.36 
TCGA-CW-5580 TCGA-CW-5589 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-5453 
       64.57        78.18       103.43        25.45        46.16         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 
       23.74        18.44        56.28        47.01        10.85        47.54 
TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
       22.52        12.69        80.19        12.26        62.63        45.96 
TCGA-EU-5907 TCGA-A4-7583 TCGA-B1-A656 TCGA-B9-A44B TCGA-BQ-5890 TCGA-BQ-7058 
        4.18         0.10         0.46         2.10         7.66        11.28 
TCGA-BQ-7061 
        7.17 

$`PBRM1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3317 
       86.10        77.85        57.17        61.58        63.95        49.02 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3365 
       52.93        45.53        88.37        42.97        10.49        28.70 
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       74.76        43.20        55.76        18.64        28.31        65.52 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3440 TCGA-AK-3443 
       84.36        73.08        66.31        15.78        57.37        46.78 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 
        2.53         3.48        19.00        65.10         5.98        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
        3.16        43.96         6.64         3.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 
        0.59         5.52        33.50         6.02        14.93        29.10 
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-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5075 
       11.64        10.29        39.45        29.03        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5088 
       43.30        11.24        11.90        34.36         7.30        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       15.09         8.05        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5119 
       90.87        52.54        29.95        19.30        17.59         1.94 
TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5697 
       18.21        37.22        14.76       112.80        48.89        60.33 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5812 
       56.94        52.77        79.36        92.98       102.48        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
       32.61        35.90         1.68        11.77        10.36        21.57 
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-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       27.55        25.05        17.19        25.55        25.91        23.01 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
       53.42        62.07        80.68        93.99        18.48        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 
       11.31        33.99        31.33        12.30        72.59        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       10.82         5.33        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       37.25        47.97         6.94        63.62        58.68        60.30 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4991 
        7.23        53.65        14.93        46.45        25.81        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-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5173 
       27.62        37.48        35.21        36.23        28.87         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        62.86        38.30 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       42.44        37.22        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4636 
       24.62        33.47        44.55        31.27         0.95        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       21.24        83.97        49.25        74.27        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
       71.87        66.21        61.91        69.86        64.18        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
       59.44        50.24        56.35        47.67        49.97        58.92 
TCGA-CJ-4907 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       49.28        45.14         3.06        63.88        72.00        79.89 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 
       25.71        25.25        18.15        62.10        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       53.42        62.66        83.77        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4856 
       66.31        74.66         1.35        83.90        18.77         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5458 
        5.46        61.41        63.42        58.82        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       55.33        10.22        21.76         2.40         1.94        31.10 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5568 
       67.96        65.65        14.63        22.78        43.69        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 
        6.77        18.21        19.63        61.05        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25        10.88         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       50.40        49.84        26.27         7.63         7.04         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.13 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         120.59          194.79 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          37.38           31.56 
[1] "0.1 - 120.6 (37.4)" "0.1 - 194.8 (31.6)"
[1] "hr=" "1.2"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        71       15        38       22
  PBRM1 WILD-TYPE     256       64       127       64
D2V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              71             256
  STAGE II             15              64
  STAGE III            38             127
  STAGE IV             22              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
  PBRM1 MUTATED    72  22  52   0
  PBRM1 WILD-TYPE 268  75 169  10
D2V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            72             268
  T2            22              75
  T3            52             169
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PBRM1 MUTATED    65   2   1
  PBRM1 WILD-TYPE 207  34   5
D2V5, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  N0            65             207
  N1             2              34
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   121  23
  PBRM1 WILD-TYPE 347  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    121   23
  PBRM1 WILD-TYPE  347   55
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0           121             347
  1            23              55
[1] 2 2
[1] FALSE
D2V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    47  99
  PBRM1 WILD-TYPE 182 340
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     47   99
  PBRM1 WILD-TYPE  182  340
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            47             182
  MALE              99             340
[1] 2 2
[1] FALSE
D2V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PBRM1 MUTATED                    1                               139
  PBRM1 WILD-TYPE                 65                               302
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PBRM1 MUTATED                                       6
  PBRM1 WILD-TYPE                                   155
D2V9, multiclass
                                       clus
vv                                      PBRM1 MUTATED PBRM1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA               139             302
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             6             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              2              40 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7963 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T      TCGA-HE-A5NI 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U      TCGA-IZ-A6M8 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
D2V11, continuous
[1] "Remove cluster labels:" "PBRM1 MUTATED"         
clus
  PBRM1 MUTATED PBRM1 WILD-TYPE 
              1              25 
     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-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117      TCGA-B9-A69E 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6      TCGA-PJ-A5Z9 
"PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" "PBRM1 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"PBRM1 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PBRM1 MUTATED                                  0     1
  PBRM1 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED                           5   136
  PBRM1 WILD-TYPE                        60   433
D2V12, multiclass
                                  clus
vv                                 PBRM1 MUTATED PBRM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    5              60
  WHITE                                      136             433
[1] 4 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
  PBRM1 MUTATED     4  99
  PBRM1 WILD-TYPE  28 342
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4   99
  PBRM1 WILD-TYPE   28  342
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 4              28
  NOT HISPANIC OR LATINO            99             342
[1] 2 2
[1] FALSE

Clustering(3) Variable = PTEN MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    19   9
  PTEN WILD-TYPE 467 166
  PTEN MUTATED PTEN WILD-TYPE 
            28            633 
  PTEN MUTATED PTEN WILD-TYPE 
             9            166 
$`PTEN MUTATED`
TCGA-KL-8323 TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 
       38.07        90.48        30.25        54.74        16.67        57.17 
TCGA-A3-3316 TCGA-AK-3427 TCGA-B0-4694 TCGA-B0-4810 TCGA-B0-4843 TCGA-B8-4621 
       49.08        84.36         3.48        15.72        11.64        25.91 
TCGA-B8-5158 TCGA-BP-4161 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4351 TCGA-BP-5010 
       20.91        90.28        53.42        49.84        31.89        28.87 
TCGA-BP-5199 TCGA-CJ-4871 TCGA-CZ-4858 TCGA-DV-5568 TCGA-EU-5907 TCGA-A4-7996 
       44.55        79.66        69.21        12.16         4.18        16.64 
TCGA-B1-A657 TCGA-B9-4115 TCGA-BQ-7051 TCGA-P4-A5E7 
        6.58        26.40        50.40        87.22 

$`PTEN WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
      141.73        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.96        84.89        98.33        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.56        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.55         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 
       10.68        74.93        79.04        92.71        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
      103.27        86.10        77.85        61.58        63.95        39.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 
        1.41         1.41         4.57         2.53        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        20.25        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
       14.30       111.02        85.51        94.72       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        64.27        54.90        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-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-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45        46.16         0.59        47.08        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       43.69        45.96        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
       18.12         3.91         6.77        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7997 
        0.10        35.18        19.13         0.89         0.23        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       24.56         3.55        16.77         0.46        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 
       30.58        34.49        12.46        50.50        28.18        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       96.92        93.34        61.28        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        99.78        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  PTEN MUTATED PTEN WILD-TYPE 
          3.48           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         90.48         194.79 
  PTEN MUTATED PTEN WILD-TYPE 
         34.98          34.29 
[1] "3.5 - 90.5 (35.0)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "1.2"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED        11        4        11        2
  PTEN WILD-TYPE     316       75       154       84
D3V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I             11            316
  STAGE II             4             75
  STAGE III           11            154
  STAGE IV             2             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  PTEN MUTATED    11   4  13   0
  PTEN WILD-TYPE 329  93 208  10
D3V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1           11            329
  T2            4             93
  T3           13            208
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PTEN MUTATED    13   3   1
  PTEN WILD-TYPE 259  33   5
D3V5, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  N0           13            259
  N1            3             33
  N2            1              5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus               0   1
  PTEN MUTATED    23   1
  PTEN WILD-TYPE 445  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     23    1
  PTEN WILD-TYPE  445   77
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           23            445
  1            1             77
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  PTEN MUTATED     8  20
  PTEN WILD-TYPE 221 419
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8   20
  PTEN WILD-TYPE  221  419
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            8            221
  MALE             20            419
[1] 2 2
[1] FALSE
D3V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PTEN MUTATED                    6                                17
  PTEN WILD-TYPE                 60                               424
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PTEN MUTATED                                       5
  PTEN WILD-TYPE                                   156
D3V9, multiclass
                                       clus
vv                                      PTEN MUTATED PTEN WILD-TYPE
  KIDNEY CHROMOPHOBE                               6             60
  KIDNEY CLEAR CELL RENAL CARCINOMA               17            424
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     1
  PTEN WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           2    25
  PTEN WILD-TYPE                        63   544
D3V12, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   2             63
  WHITE                                      25            544
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                cls
clus               0   1
  PTEN MUTATED     1  18
  PTEN WILD-TYPE  31 423
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   18
  PTEN WILD-TYPE   31  423
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1             31
  NOT HISPANIC OR LATINO           18            423
[1] 2 2
[1] FALSE

Clustering(4) Variable = BAP1 MUTATION ANALYSIS
D4V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    24  25
  BAP1 WILD-TYPE 462 150
  BAP1 MUTATED BAP1 WILD-TYPE 
            49            612 
  BAP1 MUTATED BAP1 WILD-TYPE 
            25            150 
$`BAP1 MUTATED`
TCGA-A3-3317 TCGA-AK-3451 TCGA-B0-4691 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4713 
       49.02        48.69         4.57         5.98        19.73         6.64 
TCGA-B0-4827 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       29.10        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5107 TCGA-B0-5699 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4151 TCGA-B8-5551 
       30.48        90.12         5.46        23.31        27.55         0.53 
TCGA-BP-4163 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4798 
       93.34         0.07        18.48        11.31        31.33        10.98 
TCGA-BP-4962 TCGA-BP-5174 TCGA-BP-5182 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       58.68        74.20        38.30        63.25        73.22        14.17 
TCGA-CJ-4641 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4923 
       54.61        83.97        74.27        66.21        61.91        18.81 
TCGA-CJ-5680 TCGA-CW-5580 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5469 
       25.25        64.57        18.77        61.41        58.82        31.10 
TCGA-CZ-5470 TCGA-CZ-5985 TCGA-AL-3473 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5892 
       12.69        65.65        25.08        86.76         8.88        11.97 
TCGA-MH-A560 
       30.38 

$`BAP1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.08        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       46.78        42.08        58.49        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         1.41         2.53         3.48        19.00        65.10 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14         3.16        43.96         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 
       16.77         6.02        36.53        14.93        54.48        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5094 
       11.24        11.90        34.36         7.30        25.32        10.95 
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-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       56.78        60.33        84.92        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        0.23         1.25         0.53         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       16.80        27.16        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4342 
       27.78        62.07        80.68        93.99        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       33.99        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        36.39        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30         1.78        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        74.40        49.15        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 
       34.95        31.27         0.95        59.84        46.55        75.88 
TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
       65.69        58.95        11.05        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 
       47.18        75.06        77.36        64.27        71.87        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-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-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06         4.57        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        22.32        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
       83.77         7.36        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       60.59        63.39         5.46        63.42         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        1.94        80.19        67.96        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-7173 
       12.99        12.46         9.63        58.45        30.35        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       14.86        19.27        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.78        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.07           0.10 
  BAP1 MUTATED BAP1 WILD-TYPE 
         93.34         194.79 
  BAP1 MUTATED BAP1 WILD-TYPE 
        27.550         35.065 
[1] "0.1 - 93.3 (27.6)"  "0.1 - 194.8 (35.1)"
[1] "hr=" "2.3"
D4V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BAP1 MUTATED         9        8        19       13
  BAP1 WILD-TYPE     318       71       146       73
D4V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              9            318
  STAGE II             8             71
  STAGE III           19            146
  STAGE IV            13             73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  BAP1 MUTATED    10  12  27   0
  BAP1 WILD-TYPE 330  85 194  10
D4V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1           10            330
  T2           12             85
  T3           27            194
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  BAP1 MUTATED    28   5   0
  BAP1 WILD-TYPE 244  31   6
D4V5, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  N0           28            244
  N1            5             31
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                cls
clus               0   1
  BAP1 MUTATED    34  14
  BAP1 WILD-TYPE 434  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     34   14
  BAP1 WILD-TYPE  434   64
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           34            434
  1           14             64
[1] 2 2
[1] FALSE
D4V7, binary
                cls
clus               0   1
  BAP1 MUTATED    25  24
  BAP1 WILD-TYPE 204 415
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     25   24
  BAP1 WILD-TYPE  204  415
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE           25            204
  MALE             24            415
[1] 2 2
[1] FALSE
D4V8, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             2             77 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411     TCGA-KO-8413     TCGA-AK-3430 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5843     TCGA-B4-5844 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5465 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5568 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575     TCGA-DV-5576 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5907     TCGA-A4-7286 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311     TCGA-A4-8312 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT     TCGA-A4-A57E 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP     TCGA-AL-3466 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901     TCGA-EV-5902 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793     TCGA-G7-6796 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502     TCGA-G7-A4TM 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y     TCGA-J7-8537 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"BAP1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  BAP1 MUTATED                    0                                44
  BAP1 WILD-TYPE                 66                               397
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  BAP1 MUTATED                                       5
  BAP1 WILD-TYPE                                   156
D4V9, multiclass
                                       clus
vv                                      BAP1 MUTATED BAP1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA               44            397
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     0
  BAP1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           3    44
  BAP1 WILD-TYPE                        62   525
D4V12, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   3             62
  WHITE                                      44            525
[1] 4 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
  BAP1 MUTATED     3  35
  BAP1 WILD-TYPE  29 406
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      3   35
  BAP1 WILD-TYPE   29  406
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                3             29
  NOT HISPANIC OR LATINO           35            406
[1] 2 2
[1] FALSE

Clustering(5) Variable = SETD2 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    34  24
  SETD2 WILD-TYPE 452 151
  SETD2 MUTATED SETD2 WILD-TYPE 
             58             603 
  SETD2 MUTATED SETD2 WILD-TYPE 
             24             151 
$`SETD2 MUTATED`
TCGA-KL-8337 TCGA-KM-8438 TCGA-A3-3311 TCGA-A3-3358 TCGA-A3-3383 TCGA-AK-3431 
       44.84       151.96        39.16        42.97        28.31        60.92 
TCGA-AK-3455 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 
       22.45         5.98         3.16        43.96        20.25        46.59 
TCGA-B0-4814 TCGA-B0-4822 TCGA-B0-4837 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5081 
        5.52        36.53        45.30        65.29        36.85        11.90 
TCGA-B0-5098 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5699 TCGA-B4-5835 
       52.08        18.21        21.44        14.76        90.12         0.53 
TCGA-BP-4161 TCGA-BP-4329 TCGA-BP-4343 TCGA-BP-4759 TCGA-BP-4774 TCGA-BP-4790 
       90.28        27.78        62.86        77.98        61.97        36.53 
TCGA-BP-4983 TCGA-BP-5006 TCGA-BP-5169 TCGA-BP-5178 TCGA-BP-5198 TCGA-CJ-4872 
       46.45        27.62         6.35        62.86        19.82        47.18 
TCGA-CJ-4891 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5682 TCGA-CJ-5684 
       26.93        63.88        84.66        18.87        61.91        73.35 
TCGA-CW-5580 TCGA-CW-5591 TCGA-CZ-4861 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5470 
       64.57        74.66        14.66        55.33        10.85        12.69 
TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-A656 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5876 
       29.46        12.99         0.46         2.10        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7058 
        8.88         7.66         0.95        11.28 

$`SETD2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 
       73.91        71.41        28.80        54.74        62.37        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 
       57.17        61.58        63.95        49.08        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-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       43.20        55.76        18.64        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 
       84.36        73.08        66.31        15.78        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       28.73        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4713 TCGA-B0-4714 
       19.00        65.10         2.14        19.73         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
        6.02        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        11.64 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5692 
       17.59         1.94        16.21        37.22       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 
       10.36        21.57         9.57         0.23         1.25         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       34.39        14.30       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       74.17        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-4760 
       11.31        33.99        31.33        12.30        72.59        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       10.82         5.33        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       37.02        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        33.47        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        79.66        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98        68.55        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 
       18.81        72.00        79.89        25.71        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       18.15        62.10        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       62.66        83.77         7.36        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       66.31        78.18         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       47.01        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        31.10        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23         6.81         0.16        14.86 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 
       93.34        61.28        50.40        49.84        26.27         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  SETD2 MUTATED SETD2 WILD-TYPE 
           0.46            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
         151.96          194.79 
  SETD2 MUTATED SETD2 WILD-TYPE 
         32.995          34.290 
[1] "0.5 - 152.0 (33.0)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.8"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        20        7        19       12
  SETD2 WILD-TYPE     307       72       146       74
D5V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              20             307
  STAGE II              7              72
  STAGE III            19             146
  STAGE IV             12              74
[1] 4 2
[1] 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   8  26   2
  SETD2 WILD-TYPE 318  89 195   8
D5V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            22             318
  T2             8              89
  T3            26             195
  T4             2               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  SETD2 MUTATED    27   2   1
  SETD2 WILD-TYPE 245  34   5
D5V5, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  N0            27             245
  N1             2              34
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    43  11
  SETD2 WILD-TYPE 425  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     43   11
  SETD2 WILD-TYPE  425   67
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            43             425
  1            11              67
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    16  42
  SETD2 WILD-TYPE 213 397
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     16   42
  SETD2 WILD-TYPE  213  397
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            16             213
  MALE              42             397
[1] 2 2
[1] FALSE
D5V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SETD2 MUTATED                    2                                46
  SETD2 WILD-TYPE                 64                               395
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SETD2 MUTATED                                      10
  SETD2 WILD-TYPE                                   151
D5V9, multiclass
                                       clus
vv                                      SETD2 MUTATED SETD2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                2              64
  KIDNEY CLEAR CELL RENAL CARCINOMA                46             395
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            10             151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              41 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B8-5158      TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"SETD2 WILD-TYPE" 
D5V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SETD2 MUTATED                                  0     1
  SETD2 WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED                           6    49
  SETD2 WILD-TYPE                        59   520
D5V12, multiclass
                                  clus
vv                                 SETD2 MUTATED SETD2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    6              59
  WHITE                                       49             520
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  38
  SETD2 WILD-TYPE  31 403
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   38
  SETD2 WILD-TYPE   31  403
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO            38             403
[1] 2 2
[1] FALSE

Clustering(6) Variable = KDM5C MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    17  13
  KDM5C WILD-TYPE 469 162
  KDM5C MUTATED KDM5C WILD-TYPE 
             30             631 
  KDM5C MUTATED KDM5C WILD-TYPE 
             13             162 
$`KDM5C MUTATED`
TCGA-KL-8345 TCGA-A3-3331 TCGA-AK-3430 TCGA-AK-3458 TCGA-B0-4694 TCGA-B0-4718 
       54.74        48.82        15.78        38.40         3.48        20.25 
TCGA-B0-4816 TCGA-B0-4828 TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-5077 TCGA-B0-5094 
       45.07        10.09        45.30        10.29        43.30        10.95 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5698 TCGA-B2-5641 TCGA-BP-4159 TCGA-BP-4342 
       52.54        29.95        84.92        21.57        85.51        74.17 
TCGA-BP-4351 TCGA-BP-4803 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5189 TCGA-BP-5190 
       31.89         6.71        18.51         6.35        27.02        33.24 
TCGA-BP-5202 TCGA-CJ-4871 TCGA-CW-5581 TCGA-CZ-5467 TCGA-DW-7840 TCGA-HE-A5NH 
        0.95        79.66        92.02         2.40         3.75        13.41 

$`KDM5C WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 
       49.02        48.59        36.36        37.38        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       60.92        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        4.57         2.53        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 
       19.73         3.16        43.96         6.64         3.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        52.21        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
        6.02        36.53        14.93        54.48        29.10        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        11.64 
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-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       70.52        20.94        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       52.08        15.95        62.89        90.87        90.48        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       60.33        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       21.30        11.77        10.36         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4160 
       14.27         0.53        34.39        14.30       111.02        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-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-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       45.07        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 
       37.48        35.21        36.23        28.87        48.10        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 
       33.47        19.82        44.55        34.95        31.27        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-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-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.43        17.95        68.12        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
          92.02          194.79 
  KDM5C MUTATED KDM5C WILD-TYPE 
         28.485          34.490 
[1] "0.9 - 92.0 (28.5)"  "0.1 - 194.8 (34.5)"
[1] "hr=" "2"  
D6V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        15        2         9        4
  KDM5C WILD-TYPE     312       77       156       82
D6V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              15             312
  STAGE II              2              77
  STAGE III             9             156
  STAGE IV              4              82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  KDM5C MUTATED    15   3  12   0
  KDM5C WILD-TYPE 325  94 209  10
D6V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            15             325
  T2             3              94
  T3            12             209
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM5C MUTATED    15   1   0
  KDM5C WILD-TYPE 257  35   6
D6V5, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  N0            15             257
  N1             1              35
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    24   4
  KDM5C WILD-TYPE 444  74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     24    4
  KDM5C WILD-TYPE  444   74
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            24             444
  1             4              74
[1] 2 2
[1] FALSE
D6V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     3  27
  KDM5C WILD-TYPE 226 412
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      3   27
  KDM5C WILD-TYPE  226  412
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             3             226
  MALE              27             412
[1] 2 2
[1] FALSE
D6V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              2              77 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-B0-4838 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5465 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7841 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6796 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KDM5C MUTATED                    1                                27
  KDM5C WILD-TYPE                 65                               414
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KDM5C MUTATED                                       2
  KDM5C WILD-TYPE                                   159
D6V9, multiclass
                                       clus
vv                                      KDM5C MUTATED KDM5C WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                27             414
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              41 
     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-B8-4621      TCGA-B8-5158 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B8-5164      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-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" 
D6V11, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              25 
     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-B8-5158 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117      TCGA-B9-A69E 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6      TCGA-PJ-A5Z9 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM5C WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM5C MUTATED                                  0     0
  KDM5C WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED                           2    27
  KDM5C WILD-TYPE                        63   542
D6V12, multiclass
                                  clus
vv                                 KDM5C MUTATED KDM5C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              63
  WHITE                                       27             542
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                 cls
clus                0   1
  KDM5C MUTATED     0  21
  KDM5C WILD-TYPE  32 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   21
  KDM5C WILD-TYPE   32  420
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO            21             420
[1] 2 2
[1] FALSE

Clustering(7) Variable = NEFH MUTATION ANALYSIS
D7V1, survival
                sevent
clus2              0   1
  NEFH MUTATED    13   2
  NEFH WILD-TYPE 473 173
  NEFH MUTATED NEFH WILD-TYPE 
            15            646 
  NEFH MUTATED NEFH WILD-TYPE 
             2            173 
$`NEFH MUTATED`
TCGA-AK-3451 TCGA-B0-4706 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CZ-5456 TCGA-A4-A5DU 
       48.69         2.14        18.15        62.10        56.28        16.31 
TCGA-B9-4117 TCGA-B9-A5W8 TCGA-GL-A59T TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
        0.46         6.81        17.95        73.25         5.49        19.99 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5EB 
       27.78        30.38        84.95 

$`NEFH WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 
       57.37        46.78        42.08        58.49        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       19.00        65.10         5.98        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       22.32        25.25        61.91        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NF TCGA-HE-A5NH 
        3.68        27.65         1.05        12.43        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
       11.84        56.75        16.80         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  NEFH MUTATED NEFH WILD-TYPE 
          0.46           0.07 
  NEFH MUTATED NEFH WILD-TYPE 
         84.95         194.79 
  NEFH MUTATED NEFH WILD-TYPE 
         19.99          34.44 
[1] "0.5 - 85.0 (20.0)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "1.6"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         8        3         1        1
  NEFH WILD-TYPE     319       76       164       85
D7V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              8            319
  STAGE II             3             76
  STAGE III            1            164
  STAGE IV             1             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
  NEFH MUTATED     9   4   2   0
  NEFH WILD-TYPE 331  93 219  10
D7V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            9            331
  T2            4             93
  T3            2            219
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NEFH MUTATED     2   0   0
  NEFH WILD-TYPE 270  36   6
D7V5, multiclass
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             2            312 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3380     TCGA-A3-3385 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3425     TCGA-AK-3427     TCGA-AK-3428 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AK-3450     TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4693     TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4823     TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4837     TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-4843     TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5075     TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5697     TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4169     TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4326     TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4960     TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-4986     TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-5182     TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BP-5199     TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CJ-4892     TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CJ-4918     TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5467 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
D7V6, binary
                cls
clus               0   1
  NEFH MUTATED     6   1
  NEFH WILD-TYPE 462  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      6    1
  NEFH WILD-TYPE  462   77
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            6            462
  1            1             77
[1] 2 2
[1] FALSE
D7V7, binary
                cls
clus               0   1
  NEFH MUTATED     4  11
  NEFH WILD-TYPE 225 428
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4   11
  NEFH WILD-TYPE  225  428
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            4            225
  MALE             11            428
[1] 2 2
[1] FALSE
D7V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NEFH MUTATED                    0                                 5
  NEFH WILD-TYPE                 66                               436
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NEFH MUTATED                                      10
  NEFH WILD-TYPE                                   151
D7V9, multiclass
                                       clus
vv                                      NEFH MUTATED NEFH WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                5            436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           10            151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             25 
    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-B8-5158     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-A69E 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-Q2-A5QZ 
"NEFH WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NEFH MUTATED                                  0     0
  NEFH WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED                           4     9
  NEFH WILD-TYPE                        61   560
D7V12, multiclass
                                  clus
vv                                 NEFH MUTATED NEFH WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   4             61
  WHITE                                       9            560
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                cls
clus               0   1
  NEFH MUTATED     0  12
  NEFH WILD-TYPE  32 429
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0   12
  NEFH WILD-TYPE   32  429
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO           12            429
[1] 2 2
[1] FALSE

Clustering(8) Variable = VHL MUTATION ANALYSIS
D8V1, survival
               sevent
clus2             0   1
  VHL MUTATED   120  54
  VHL WILD-TYPE 366 121
  VHL MUTATED VHL WILD-TYPE 
          174           487 
  VHL MUTATED VHL WILD-TYPE 
           54           121 
$`VHL MUTATED`
TCGA-KN-8432 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 
        2.50        48.82        45.53        51.25        53.29        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3455 TCGA-AK-3458 TCGA-AS-3778 
       18.64        28.31        65.52        22.45        38.40         1.41 
TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4810 
       65.10         2.14        19.73        43.96         6.64        15.72 
TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4828 
        5.52        16.77         6.02        14.93        29.10        10.09 
TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5081 
       56.68        26.07        36.85        70.52        43.30        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       25.32        18.51         8.05         2.24        21.86        15.95 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5113 TCGA-B0-5115 
       90.87        52.54        30.48        29.95        11.80        26.20 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       14.76       112.80        48.89       101.13        46.68        56.78 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       39.55       120.59       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-5635 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5843 
       97.41        35.90        10.36         0.23         4.64         0.36 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5162 
       27.16        27.55        25.05        24.66        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4159 TCGA-BP-4164 
       27.02        24.23         6.38         0.53        85.51        32.61 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4341 TCGA-BP-4771 TCGA-BP-4807 TCGA-BP-4960 
       89.36        27.78        52.24         5.33         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
       14.24         7.23        47.11        53.65        14.93        33.34 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4995 
       25.81        27.22         3.88        46.45        16.47        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        36.23         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        49.15        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       37.25        22.78        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       33.47        19.82        44.55        59.84        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4875 TCGA-CJ-4894 TCGA-CJ-4900 TCGA-CJ-4903 
       14.17        11.05        77.36        27.65        56.35        51.29 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5672 
       50.33        54.48        45.14         3.06         4.57        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       84.66        25.71        25.25        73.35        67.00        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       75.58        62.66        83.77         7.36        64.57        81.83 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       66.31        74.66        83.90       103.43        25.45         0.59 
TCGA-CZ-4861 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
       14.66        56.94        47.01        47.54        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        14.63        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-AL-3473 TCGA-BQ-5892 
       18.12         3.91         6.77         4.18        25.08        11.97 

$`VHL WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3357 
       49.02        48.59        36.36        37.38        52.93        88.37 
TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 
       42.97        10.49        28.70        74.63        74.76        43.20 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       60.92        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 
       58.49        48.69        45.93        28.73        37.58        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       28.04        12.13        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        3.48        19.00         5.98         3.16         3.25        20.25 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4822 
       46.59         0.59        52.21        45.07        33.50        36.53 
TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       54.48        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        11.64        10.29        65.29        39.45        29.03 
TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5092 
        2.27        20.94        11.24        34.36         7.30        15.09 
TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5109 TCGA-B0-5110 
       10.95        52.08        62.89        90.48        19.30        35.90 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       37.22        15.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-4098 
       52.77        79.36        92.98        89.49        32.61         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5834 
       12.30        21.30        11.77        21.57         9.57         1.25 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4619 
        0.53         5.46         0.23        23.31        16.80        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5545 
       25.55        25.91        23.01        20.91         0.85        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4160 
       16.60        14.27        34.39        14.30       111.02        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       90.28       101.06        93.34        99.85         0.43        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-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
       62.07        80.68         0.07        93.99        18.48        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       13.15        10.82        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4962 
       10.98        37.25        36.95         6.71        47.97        58.68 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4985 
       48.89        49.38        45.50        36.07        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5168 
       36.95         5.82        43.00        18.51        28.87        48.10 
TCGA-BP-5178 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5191 
       62.86        38.30        37.22        13.35        27.02        31.79 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 
       34.95        31.27         0.95        46.55        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       63.98        68.55        26.93        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
       59.44        50.24        47.67        49.97        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5678 
       49.28        38.56        18.81        63.88        79.89        18.87 
TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 
       22.32        18.15        61.91        62.10        53.42        92.02 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 
       85.78        78.18         1.35        18.77        46.16        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       69.21        58.75        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 
       55.33        55.33        10.85        10.22        21.76        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
        2.40         1.94        22.78        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-A4-7286 TCGA-A4-7287 
       11.67        66.28        56.84        23.90        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
        9.63        58.45        30.35        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  VHL MUTATED VHL WILD-TYPE 
         0.23          0.07 
  VHL MUTATED VHL WILD-TYPE 
       120.59        194.79 
  VHL MUTATED VHL WILD-TYPE 
        33.29         34.39 
[1] "0.2 - 120.6 (33.3)" "0.1 - 194.8 (34.4)"
[1] "hr=" "1.3"
D8V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED        94       15        42       23
  VHL WILD-TYPE     233       64       123       63
D8V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I            94           233
  STAGE II           15            64
  STAGE III          42           123
  STAGE IV           23            63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  VHL MUTATED    95  19  56   4
  VHL WILD-TYPE 245  78 165   6
D8V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1          95           245
  T2          19            78
  T3          56           165
  T4           4             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    77   5   0
  VHL WILD-TYPE 195  31   6
D8V5, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  N0          77           195
  N1           5            31
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
               cls
clus              0   1
  VHL MUTATED   150  23
  VHL WILD-TYPE 318  55
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    150   23
  VHL WILD-TYPE  318   55
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0         150           318
  1          23            55
[1] 2 2
[1] FALSE
D8V7, binary
               cls
clus              0   1
  VHL MUTATED    65 109
  VHL WILD-TYPE 164 330
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     65  109
  VHL WILD-TYPE  164  330
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          65           164
  MALE           109           330
[1] 2 2
[1] FALSE
D8V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  VHL MUTATED                    1                               171
  VHL WILD-TYPE                 65                               270
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  VHL MUTATED                                       2
  VHL WILD-TYPE                                   159
D8V9, multiclass
                                       clus
vv                                      VHL MUTATED VHL WILD-TYPE
  KIDNEY CHROMOPHOBE                              1            65
  KIDNEY CLEAR CELL RENAL CARCINOMA             171           270
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           2           159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  VHL MUTATED                                  0     2
  VHL WILD-TYPE                                2     9
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED                           2   167
  VHL WILD-TYPE                        63   402
D8V12, multiclass
                                  clus
vv                                 VHL MUTATED VHL WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      2             9
  BLACK OR AFRICAN AMERICAN                  2            63
  WHITE                                    167           402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
               cls
clus              0   1
  VHL MUTATED     9 112
  VHL WILD-TYPE  23 329
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      9  112
  VHL WILD-TYPE   23  329
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               9            23
  NOT HISPANIC OR LATINO         112           329
[1] 2 2
[1] FALSE

Clustering(9) Variable = NF2 MUTATION ANALYSIS
D9V1, survival
               sevent
clus2             0   1
  NF2 MUTATED    11   5
  NF2 WILD-TYPE 475 170
  NF2 MUTATED NF2 WILD-TYPE 
           16           645 
  NF2 MUTATED NF2 WILD-TYPE 
            5           170 
$`NF2 MUTATED`
TCGA-B0-5084 TCGA-B0-5098 TCGA-B8-4153 TCGA-BP-4986 TCGA-CJ-4638 TCGA-CJ-4901 
        7.30        52.08        25.05        25.81        14.17        47.67 
TCGA-A4-8098 TCGA-B1-A47M TCGA-B9-4117 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 
       29.46        21.67         0.46        86.76         8.88         2.76 
TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 TCGA-P4-A5EA 
       19.00        25.15         3.68         6.61 

$`NF2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90        34.36        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 
        0.23        23.31        16.80        27.16        27.55        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        31.30        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       25.08        44.61         2.20        19.56        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       14.86        19.27        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.88        51.19        61.02        54.90        34.19        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       34.82        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        99.78        87.22        42.94        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  NF2 MUTATED NF2 WILD-TYPE 
         0.46          0.07 
  NF2 MUTATED NF2 WILD-TYPE 
        86.76        194.79 
  NF2 MUTATED NF2 WILD-TYPE 
       20.335        34.950 
[1] "0.5 - 86.8 (20.3)"  "0.1 - 194.8 (35.0)"
[1] "hr=" "2"  
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         4        0         7        4
  NF2 WILD-TYPE     323       79       158       82
D9V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             4           323
  STAGE II            0            79
  STAGE III           7           158
  STAGE IV            4            82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  NF2 MUTATED     5   1  10   0
  NF2 WILD-TYPE 335  96 211  10
D9V4, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  T1           5           335
  T2           1            96
  T3          10           211
  T4           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  NF2 MUTATED     1   6   0
  NF2 WILD-TYPE 271  30   6
D9V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           1           271
  N1           6            30
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
               cls
clus              0   1
  NF2 MUTATED     6   4
  NF2 WILD-TYPE 462  74
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      6    4
  NF2 WILD-TYPE  462   74
   clus
vv  NF2 MUTATED NF2 WILD-TYPE
  0           6           462
  1           4            74
[1] 2 2
[1] FALSE
D9V7, binary
               cls
clus              0   1
  NF2 MUTATED     6  10
  NF2 WILD-TYPE 223 429
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      6   10
  NF2 WILD-TYPE  223  429
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           6           223
  MALE            10           429
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            77 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KO-8411 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B4-5844    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4861 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EU-5907    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X    TCGA-IA-A40Y 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NF2 MUTATED                    0                                 6
  NF2 WILD-TYPE                 66                               435
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NF2 MUTATED                                      10
  NF2 WILD-TYPE                                   151
D9V9, multiclass
                                       clus
vv                                      NF2 MUTATED NF2 WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               6           435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA          10           151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            41 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KO-8416    TCGA-B8-4621    TCGA-B8-5158    TCGA-B8-5164    TCGA-A4-8310 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4115    TCGA-B9-7268    TCGA-B9-A44B 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7963    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IA-A40U    TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" 
D9V11, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            1            25 
   TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409    TCGA-B8-5158    TCGA-A4-A48D 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7963    TCGA-G7-7501    TCGA-GL-7773 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-HE-A5NI    TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF2 MUTATED                                  0     0
  NF2 WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF2 MUTATED                           5    10
  NF2 WILD-TYPE                        60   559
D9V12, multiclass
                                  clus
vv                                 NF2 MUTATED NF2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  5            60
  WHITE                                     10           559
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
               cls
clus              0   1
  NF2 MUTATED     2  11
  NF2 WILD-TYPE  30 430
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2   11
  NF2 WILD-TYPE   30  430
                        clus
vv                       NF2 MUTATED NF2 WILD-TYPE
  HISPANIC OR LATINO               2            30
  NOT HISPANIC OR LATINO          11           430
[1] 2 2
[1] FALSE

Clustering(10) Variable = HNRNPM MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2                0   1
  HNRNPM MUTATED    11   1
  HNRNPM WILD-TYPE 475 174
  HNRNPM MUTATED HNRNPM WILD-TYPE 
              12              649 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
               1              174 
$`HNRNPM MUTATED`
TCGA-KM-8441 TCGA-BP-5010 TCGA-BQ-5887 TCGA-BQ-7055 TCGA-BQ-7062 TCGA-DW-7841 
       28.80        28.87        25.35        26.27         3.81        14.63 
TCGA-DZ-6132 TCGA-EV-5902 TCGA-G7-7502 TCGA-GL-6846 TCGA-IA-A40X TCGA-PJ-A5Z8 
       80.88        19.00        25.84       194.79        19.99        12.85 

$`HNRNPM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 
       37.02        27.62        37.48        35.21        36.23        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        50.40        49.84        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.04         7.17        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       24.46        13.78         3.75         3.02        40.77        79.86 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        54.90        34.19        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.15        13.68         6.38        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 
       56.75        73.25         5.49        16.80         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
       87.22        42.94         6.61        84.95        92.58        17.75 
TCGA-Q2-A5QZ 
       14.07 

  HNRNPM MUTATED HNRNPM WILD-TYPE 
            3.81             0.07 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          194.79           151.96 
  HNRNPM MUTATED HNRNPM WILD-TYPE 
          25.595           34.820 
[1] "3.8 - 194.8 (25.6)" "0.1 - 152.0 (34.8)"
[1] "hr=" "2.6"
D10V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  HNRNPM MUTATED         9        0         2        1
  HNRNPM WILD-TYPE     318       79       163       85
D10V3, multiclass
           clus
vv          HNRNPM MUTATED HNRNPM WILD-TYPE
  STAGE I                9              318
  STAGE II               0               79
  STAGE III              2              163
  STAGE IV               1               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
  HNRNPM MUTATED     9   0   2   1
  HNRNPM WILD-TYPE 331  97 219   9
D10V4, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  T1              9              331
  T2              0               97
  T3              2              219
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  HNRNPM MUTATED     2   1   0
  HNRNPM WILD-TYPE 270  35   6
D10V5, multiclass
    clus
vv   HNRNPM MUTATED HNRNPM WILD-TYPE
  N0              2              270
  N1              1               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     6   0
  HNRNPM WILD-TYPE 462  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      6    0
  HNRNPM WILD-TYPE  462   78
   clus
vv  HNRNPM MUTATED HNRNPM WILD-TYPE
  0              6              462
  1              0               78
[1] 2 2
[1] FALSE
D10V7, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     3   9
  HNRNPM WILD-TYPE 226 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      3    9
  HNRNPM WILD-TYPE  226  430
        clus
vv       HNRNPM MUTATED HNRNPM WILD-TYPE
  FEMALE              3              226
  MALE                9              430
[1] 2 2
[1] FALSE
D10V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  HNRNPM MUTATED                    1                                 1
  HNRNPM WILD-TYPE                 65                               440
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  HNRNPM MUTATED                                      10
  HNRNPM WILD-TYPE                                   151
D10V9, multiclass
                                       clus
vv                                      HNRNPM MUTATED HNRNPM WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             10              151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNRNPM MUTATED                                  0     0
  HNRNPM WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  HNRNPM MUTATED                           3     8
  HNRNPM WILD-TYPE                        62   561
D10V12, multiclass
                                  clus
vv                                 HNRNPM MUTATED HNRNPM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               62
  WHITE                                         8              561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                  cls
clus                 0   1
  HNRNPM MUTATED     0   8
  HNRNPM WILD-TYPE  32 433
[1] "tbl2"
                  cls
clus               [,1] [,2]
  HNRNPM MUTATED      0    8
  HNRNPM WILD-TYPE   32  433
                        clus
vv                       HNRNPM MUTATED HNRNPM WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              8              433
[1] 2 2
[1] FALSE

Clustering(11) Variable = MET MUTATION ANALYSIS
D11V1, survival
               sevent
clus2             0   1
  MET MUTATED    16   3
  MET WILD-TYPE 470 172
  MET MUTATED MET WILD-TYPE 
           19           642 
  MET MUTATED MET WILD-TYPE 
            3           172 
$`MET MUTATED`
TCGA-B0-5098 TCGA-B0-5707 TCGA-CW-6087 TCGA-EU-5907 TCGA-A4-7734 TCGA-A4-7997 
       52.08        92.98         1.35         4.18         0.89        30.48 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A654 TCGA-B9-4117 TCGA-BQ-5882 TCGA-BQ-7059 
       30.35        44.61         3.55         0.46        21.63         7.63 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-GL-A59R TCGA-HE-A5NH TCGA-IA-A40U TCGA-IZ-8196 
       80.88        54.90        12.43        13.41        16.80        21.34 
TCGA-MH-A561 
       27.65 

$`MET WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-A4-7286 TCGA-A4-7287 
       23.90        18.12         3.91         6.77        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7915 TCGA-A4-7996 
       61.05         0.10        35.18        19.13         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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A655 
       25.08         2.20        19.56        21.67        24.56        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 
       12.46        50.50        28.18        26.40        20.61        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7061 
       50.40        49.84        26.27        11.28         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        61.02        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI 
        3.68        27.65         1.05        17.95        68.12        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       56.75        73.25         5.49        19.99         2.04        22.26 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.78        30.38        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  MET MUTATED MET WILD-TYPE 
         0.46          0.07 
  MET MUTATED MET WILD-TYPE 
        92.98        194.79 
  MET MUTATED MET WILD-TYPE 
       21.340        34.885 
[1] "0.5 - 93.0 (21.3)"  "0.1 - 194.8 (34.9)"
[1] "hr=" "1.2"
D11V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MET MUTATED        11        0         4        2
  MET WILD-TYPE     316       79       161       84
D11V3, multiclass
           clus
vv          MET MUTATED MET WILD-TYPE
  STAGE I            11           316
  STAGE II            0            79
  STAGE III           4           161
  STAGE IV            2            84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  MET MUTATED    11   2   6   0
  MET WILD-TYPE 329  95 215  10
D11V4, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  T1          11           329
  T2           2            95
  T3           6           215
  T4           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  MET MUTATED     5   1   1
  MET WILD-TYPE 267  35   5
D11V5, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  N0           5           267
  N1           1            35
  N2           1             5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
               cls
clus              0   1
  MET MUTATED     9   1
  MET WILD-TYPE 459  77
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      9    1
  MET WILD-TYPE  459   77
   clus
vv  MET MUTATED MET WILD-TYPE
  0           9           459
  1           1            77
[1] 2 2
[1] FALSE
D11V7, binary
               cls
clus              0   1
  MET MUTATED     6  13
  MET WILD-TYPE 223 426
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      6   13
  MET WILD-TYPE  223  426
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           6           223
  MALE            13           426
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            2            77 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KO-8411 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B4-5844    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4861 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X    TCGA-IA-A40Y 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-J7-8537    TCGA-Q2-A5QZ 
"MET WILD-TYPE" "MET WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MET MUTATED                    0                                 4
  MET WILD-TYPE                 66                               437
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MET MUTATED                                      15
  MET WILD-TYPE                                   146
D11V9, multiclass
                                       clus
vv                                      MET MUTATED MET WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               4           437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA          15           146
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MET MUTATED                                  0     0
  MET WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  MET MUTATED                           4    11
  MET WILD-TYPE                        61   558
D11V12, multiclass
                                  clus
vv                                 MET MUTATED MET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  4            61
  WHITE                                     11           558
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
               cls
clus              0   1
  MET MUTATED     1  14
  MET WILD-TYPE  31 427
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      1   14
  MET WILD-TYPE   31  427
                        clus
vv                       MET MUTATED MET WILD-TYPE
  HISPANIC OR LATINO               1            31
  NOT HISPANIC OR LATINO          14           427
[1] 2 2
[1] FALSE

Clustering(12) Variable = MUC5B MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2               0   1
  MUC5B MUTATED    22   7
  MUC5B WILD-TYPE 464 168
  MUC5B MUTATED MUC5B WILD-TYPE 
             29             632 
  MUC5B MUTATED MUC5B WILD-TYPE 
              7             168 
$`MUC5B MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8335 TCGA-KL-8339 
       38.07       141.73        90.48       108.62        92.55        28.11 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8416 TCGA-B8-4153 
        0.99        52.27        74.93        80.38        61.58        25.05 
TCGA-CJ-4902 TCGA-CW-5580 TCGA-CW-5581 TCGA-DV-5569 TCGA-A4-7288 TCGA-A4-8311 
       49.97        64.57        92.02        11.67        61.05        23.97 
TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-A47N 
       19.73         8.48         8.28        12.99         9.63        24.56 
TCGA-BQ-5888 TCGA-BQ-7044 TCGA-BQ-7062 TCGA-DW-7963 TCGA-P4-A5E7 
       13.25       123.62         3.81        40.77        87.22 

$`MUC5B WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22       137.06       102.81        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.33        96.95        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 
       25.48        25.91        65.19       104.52         3.55        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-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8417 
       87.78       103.27        86.10        77.85        57.17        63.95 
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.02        48.59        36.36        37.38 
TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       48.82        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 
       55.76        18.64        28.31        65.52        20.28       109.91 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.16        27.55        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       83.77         7.36        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       43.69        45.96        12.16        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       30.48        29.46        25.64        23.28        23.31        19.63 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       14.33        12.46        16.96        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        25.35        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
        7.66         0.95        11.97         7.92         2.76        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.04         7.17        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       99.78        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  MUC5B MUTATED MUC5B WILD-TYPE 
           0.99            0.07 
  MUC5B MUTATED MUC5B WILD-TYPE 
         141.73          194.79 
  MUC5B MUTATED MUC5B WILD-TYPE 
          40.77           34.09 
[1] "1.0 - 141.7 (40.8)" "0.1 - 194.8 (34.1)"
[1] "hr=" "1.3"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MUC5B MUTATED        11        5         8        5
  MUC5B WILD-TYPE     316       74       157       81
D12V3, multiclass
           clus
vv          MUC5B MUTATED MUC5B WILD-TYPE
  STAGE I              11             316
  STAGE II              5              74
  STAGE III             8             157
  STAGE IV              5              81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  MUC5B MUTATED    14   5  10   1
  MUC5B WILD-TYPE 326  92 211   9
D12V4, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  T1            14             326
  T2             5              92
  T3            10             211
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MUC5B MUTATED    10   4   0
  MUC5B WILD-TYPE 262  32   6
D12V5, multiclass
    clus
vv   MUC5B MUTATED MUC5B WILD-TYPE
  N0            10             262
  N1             4              32
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                 cls
clus                0   1
  MUC5B MUTATED    16   4
  MUC5B WILD-TYPE 452  74
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     16    4
  MUC5B WILD-TYPE  452   74
   clus
vv  MUC5B MUTATED MUC5B WILD-TYPE
  0            16             452
  1             4              74
[1] 2 2
[1] FALSE
D12V7, binary
                 cls
clus                0   1
  MUC5B MUTATED    11  19
  MUC5B WILD-TYPE 218 420
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED     11   19
  MUC5B WILD-TYPE  218  420
        clus
vv       MUC5B MUTATED MUC5B WILD-TYPE
  FEMALE            11             218
  MALE              19             420
[1] 2 2
[1] FALSE
D12V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MUC5B MUTATED                   11                                 5
  MUC5B WILD-TYPE                 55                               436
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MUC5B MUTATED                                      14
  MUC5B WILD-TYPE                                   147
D12V9, multiclass
                                       clus
vv                                      MUC5B MUTATED MUC5B WILD-TYPE
  KIDNEY CHROMOPHOBE                               11              55
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            14             147
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MUC5B MUTATED                                  0     1
  MUC5B WILD-TYPE                                2    10
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MUC5B MUTATED                           4    25
  MUC5B WILD-TYPE                        61   544
D12V12, multiclass
                                  clus
vv                                 MUC5B MUTATED MUC5B WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        1              10
  BLACK OR AFRICAN AMERICAN                    4              61
  WHITE                                       25             544
[1] 4 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
  MUC5B MUTATED     1  20
  MUC5B WILD-TYPE  31 421
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC5B MUTATED      1   20
  MUC5B WILD-TYPE   31  421
                        clus
vv                       MUC5B MUTATED MUC5B WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO            20             421
[1] 2 2
[1] FALSE

Clustering(13) Variable = KDM6A MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     6   2
  KDM6A WILD-TYPE 480 173
  KDM6A MUTATED KDM6A WILD-TYPE 
              8             653 
  KDM6A MUTATED KDM6A WILD-TYPE 
              2             173 
$`KDM6A MUTATED`
TCGA-B0-5075 TCGA-B2-4098 TCGA-BP-4765 TCGA-CZ-5465 TCGA-A4-A48D TCGA-BQ-5886 
       20.94         1.68        71.80        47.54        12.46        26.04 
TCGA-BQ-7060 TCGA-IZ-A6M8 
        7.04        16.34 

$`KDM6A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 
       26.07        29.03         2.27        36.85        70.52        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4766 
       77.98        77.62         5.98        44.15        41.75        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 
       55.33        47.01        10.85        10.22        21.76        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-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-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 
       49.84        26.27        11.28         7.63         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       16.80        19.99         2.04        22.26        21.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  KDM6A MUTATED KDM6A WILD-TYPE 
           1.68            0.07 
  KDM6A MUTATED KDM6A WILD-TYPE 
          71.80          194.79 
  KDM6A MUTATED KDM6A WILD-TYPE 
          18.64           34.39 
[1] "1.7 - 71.8 (18.6)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "1.5"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         7        0         4        0
  KDM6A WILD-TYPE     320       79       161       86
D13V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               7             320
  STAGE II              0              79
  STAGE III             4             161
  STAGE IV              0              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
  KDM6A MUTATED     6   1   4   0
  KDM6A WILD-TYPE 334  96 217  10
D13V4, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T1             6             334
  T2             1              96
  T3             4             217
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  KDM6A MUTATED     1   0   0
  KDM6A WILD-TYPE 271  36   6
D13V5, multiclass
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5EA 
"KDM6A WILD-TYPE" 
D13V6, binary
                 cls
clus                0   1
  KDM6A MUTATED     8   0
  KDM6A WILD-TYPE 460  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      8    0
  KDM6A WILD-TYPE  460   78
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             8             460
  1             0              78
[1] 2 2
[1] FALSE
D13V7, binary
                 cls
clus                0   1
  KDM6A MUTATED     4   7
  KDM6A WILD-TYPE 225 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      4    7
  KDM6A WILD-TYPE  225  432
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             4             225
  MALE               7             432
[1] 2 2
[1] FALSE
D13V8, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KDM6A MUTATED                    0                                 4
  KDM6A WILD-TYPE                 66                               437
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KDM6A MUTATED                                       7
  KDM6A WILD-TYPE                                   154
D13V9, multiclass
                                       clus
vv                                      KDM6A MUTATED KDM6A WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 4             437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             7             154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              2              40 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B8-5158      TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A57E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9      TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
D13V11, continuous
[1] "Remove cluster labels:" "KDM6A MUTATED"         
clus
  KDM6A MUTATED KDM6A WILD-TYPE 
              1              25 
     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-B8-5158      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117      TCGA-B9-A69E 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6      TCGA-PJ-A5Z9 
"KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" "KDM6A WILD-TYPE" 
     TCGA-Q2-A5QZ 
"KDM6A WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KDM6A MUTATED                                  1     0
  KDM6A WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED                           4     3
  KDM6A WILD-TYPE                        61   566
D13V12, multiclass
                                  clus
vv                                 KDM6A MUTATED KDM6A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    4              61
  WHITE                                        3             566
[1] 4 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
  KDM6A MUTATED     0   6
  KDM6A WILD-TYPE  32 435
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    6
  KDM6A WILD-TYPE   32  435
                        clus
vv                       KDM6A MUTATED KDM6A WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             6             435
[1] 2 2
[1] FALSE

Clustering(14) Variable = TDG MUTATION ANALYSIS
D14V1, survival
               sevent
clus2             0   1
  TDG MUTATED     5   0
  TDG WILD-TYPE 481 175
  TDG MUTATED TDG WILD-TYPE 
            5           656 
  TDG MUTATED TDG WILD-TYPE 
            0           175 
$`TDG MUTATED`
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-7840 TCGA-GL-6846 
        0.95        11.97        96.92         3.75       194.79 

$`TDG WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.88         7.66         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
      129.86        37.55        24.46        13.78        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       25.84         6.38        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  TDG MUTATED TDG WILD-TYPE 
         0.95          0.07 
  TDG MUTATED TDG WILD-TYPE 
       194.79        151.96 
  TDG MUTATED TDG WILD-TYPE 
       11.970        34.325 
[1] "0.9 - 194.8 (12.0)" "0.1 - 152.0 (34.3)"
[1] "hr="     "3300000"
D14V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  TDG MUTATED         3        0         1        1
  TDG WILD-TYPE     324       79       164       85
D14V3, multiclass
           clus
vv          TDG MUTATED TDG WILD-TYPE
  STAGE I             3           324
  STAGE II            0            79
  STAGE III           1           164
  STAGE IV            1            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
  TDG MUTATED     3   0   1   1
  TDG WILD-TYPE 337  97 220   9
D14V4, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  T1           3           337
  T2           0            97
  T3           1           220
  T4           1             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  TDG MUTATED     2   1   0
  TDG WILD-TYPE 270  35   6
D14V5, multiclass
    clus
vv   TDG MUTATED TDG WILD-TYPE
  N0           2           270
  N1           1            35
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
               cls
clus              0   1
  TDG MUTATED     3   0
  TDG WILD-TYPE 465  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      3    0
  TDG WILD-TYPE  465   78
   clus
vv  TDG MUTATED TDG WILD-TYPE
  0           3           465
  1           0            78
[1] 2 2
[1] FALSE
D14V7, binary
               cls
clus              0   1
  TDG MUTATED     1   4
  TDG WILD-TYPE 228 435
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      1    4
  TDG WILD-TYPE  228  435
        clus
vv       TDG MUTATED TDG WILD-TYPE
  FEMALE           1           228
  MALE             4           435
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "TDG MUTATED"           
clus
  TDG MUTATED TDG WILD-TYPE 
            1            78 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KO-8411 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-B4-5844    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4861 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-EU-5907    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"TDG WILD-TYPE" "TDG WILD-TYPE" "TDG WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TDG MUTATED                    0                                 0
  TDG WILD-TYPE                 66                               441
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TDG MUTATED                                       5
  TDG WILD-TYPE                                   156
D14V9, multiclass
                                       clus
vv                                      TDG MUTATED TDG WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               0           441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           5           156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TDG MUTATED                                  0     0
  TDG WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  TDG MUTATED                           1     4
  TDG WILD-TYPE                        64   565
D14V12, multiclass
                                  clus
vv                                 TDG MUTATED TDG WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            64
  WHITE                                      4           565
[1] 4 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
  TDG MUTATED     0   4
  TDG WILD-TYPE  32 437
[1] "tbl2"
               cls
clus            [,1] [,2]
  TDG MUTATED      0    4
  TDG WILD-TYPE   32  437
                        clus
vv                       TDG MUTATED TDG WILD-TYPE
  HISPANIC OR LATINO               0            32
  NOT HISPANIC OR LATINO           4           437
[1] 2 2
[1] FALSE

Clustering(15) Variable = NFE2L2 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  NFE2L2 MUTATED     7   3
  NFE2L2 WILD-TYPE 479 172
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              10              651 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               3              172 
$`NFE2L2 MUTATED`
TCGA-B0-4837 TCGA-B0-5097 TCGA-B2-4098 TCGA-BP-4768 TCGA-BP-5178 TCGA-CZ-5456 
       45.30        21.86         1.68        13.15        62.86        56.28 
TCGA-B1-A47M TCGA-BQ-5881 TCGA-BQ-7044 TCGA-BQ-7051 
       21.67        47.80       123.62        50.40 

$`NFE2L2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       10.09        78.44        40.70        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 
       89.49        61.32        97.41        32.61        35.90        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        1.78        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       30.35        25.08        44.61         2.20        19.56        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92         2.76        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       93.34        61.28        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            1.68             0.07 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          123.62           194.79 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           46.55            34.19 
[1] "1.7 - 123.6 (46.5)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.1"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         4        2         3        1
  NFE2L2 WILD-TYPE     323       77       162       85
D15V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                4              323
  STAGE II               2               77
  STAGE III              3              162
  STAGE IV               1               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
  NFE2L2 MUTATED     4   2   4   0
  NFE2L2 WILD-TYPE 336  95 217  10
D15V4, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1              4              336
  T2              2               95
  T3              4              217
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  NFE2L2 MUTATED     5   0   0
  NFE2L2 WILD-TYPE 267  36   6
D15V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              5              267
  N1              0               36
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     8   1
  NFE2L2 WILD-TYPE 460  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      8    1
  NFE2L2 WILD-TYPE  460   77
   clus
vv  NFE2L2 MUTATED NFE2L2 WILD-TYPE
  0              8              460
  1              1               77
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     3   7
  NFE2L2 WILD-TYPE 226 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      3    7
  NFE2L2 WILD-TYPE  226  432
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              3              226
  MALE                7              432
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               1               78 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5457       TCGA-CZ-5465 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       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-G7-6790       TCGA-G7-6793 
"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-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 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NFE2L2 MUTATED                    0                                 6
  NFE2L2 WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NFE2L2 MUTATED                                       4
  NFE2L2 WILD-TYPE                                   157
D15V9, multiclass
                                       clus
vv                                      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFE2L2 MUTATED                                  0     0
  NFE2L2 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED                           2     8
  NFE2L2 WILD-TYPE                        63   561
D15V12, multiclass
                                  clus
vv                                 NFE2L2 MUTATED NFE2L2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               63
  WHITE                                         8              561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                  cls
clus                 0   1
  NFE2L2 MUTATED     0   5
  NFE2L2 WILD-TYPE  32 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0    5
  NFE2L2 WILD-TYPE   32  436
                        clus
vv                       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(16) Variable = ATM MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  ATM MUTATED    11   5
  ATM WILD-TYPE 475 170
  ATM MUTATED ATM WILD-TYPE 
           16           645 
  ATM MUTATED ATM WILD-TYPE 
            5           170 
$`ATM MUTATED`
TCGA-KL-8324 TCGA-KN-8428 TCGA-KN-8435 TCGA-B0-4690 TCGA-B0-5097 TCGA-B0-5703 
      141.73        52.27       115.00         1.41        21.86        39.55 
TCGA-BP-4964 TCGA-BP-5173 TCGA-CJ-4639 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-5686 
       61.22         1.78        75.88        56.35        58.92        67.00 
TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 TCGA-A4-7997 
       14.66        63.42        12.26        30.48 

$`ATM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 
       25.91        65.19       104.52         3.55         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 
       19.33         2.50        11.21        59.08        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 
       61.58        63.95        39.16        49.08        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       60.92        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        4.57         2.53         3.48        19.00        65.10         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5098 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        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       56.94        52.77       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       63.25        73.22        14.17        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        59.44        50.24        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        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       61.91        62.10        73.35        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       69.21        58.75        60.59        63.39         5.46        61.41 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        67.96        65.65        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  ATM MUTATED ATM WILD-TYPE 
         1.41          0.07 
  ATM MUTATED ATM WILD-TYPE 
       141.73        194.79 
  ATM MUTATED ATM WILD-TYPE 
        54.31         33.99 
[1] "1.4 - 141.7 (54.3)" "0.1 - 194.8 (34.0)"
[1] "hr=" "1"  
D16V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         6        6         1        3
  ATM WILD-TYPE     321       73       164       83
D16V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             6           321
  STAGE II            6            73
  STAGE III           1           164
  STAGE IV            3            83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             T1  T2  T3  T4
  ATM MUTATED     6   6   2   2
  ATM WILD-TYPE 334  91 219   8
D16V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           6           334
  T2           6            91
  T3           2           219
  T4           2             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  ATM MUTATED     8   2   0
  ATM WILD-TYPE 264  34   6
D16V5, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  N0           8           264
  N1           2            34
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
               cls
clus              0   1
  ATM MUTATED    11   3
  ATM WILD-TYPE 457  75
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     11    3
  ATM WILD-TYPE  457   75
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          11           457
  1           3            75
[1] 2 2
[1] FALSE
D16V7, binary
               cls
clus              0   1
  ATM MUTATED     7   9
  ATM WILD-TYPE 222 430
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      7    9
  ATM WILD-TYPE  222  430
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           7           222
  MALE             9           430
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            78 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KO-8411 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B4-5844    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4862 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469    TCGA-CZ-5982 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569    TCGA-DV-5574 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905    TCGA-EU-5907 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8312 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E    TCGA-A4-A5DU 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-DW-7963    TCGA-EV-5901    TCGA-EV-5902 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6790    TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-6797 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40U    TCGA-IA-A40X 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ATM MUTATED                    3                                12
  ATM WILD-TYPE                 63                               429
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ATM MUTATED                                       1
  ATM WILD-TYPE                                   160
D16V9, multiclass
                                       clus
vv                                      ATM MUTATED ATM WILD-TYPE
  KIDNEY CHROMOPHOBE                              3            63
  KIDNEY CLEAR CELL RENAL CARCINOMA              12           429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           1           160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            2            40 
   TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409    TCGA-KO-8416    TCGA-B8-4621 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B8-5158    TCGA-B8-5164    TCGA-A4-8310    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-3466    TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268    TCGA-B9-A44B    TCGA-B9-A69E 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7963    TCGA-G7-7501    TCGA-GL-7773 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-GL-A59T    TCGA-HE-A5NI    TCGA-HE-A5NJ    TCGA-HE-A5NK    TCGA-IA-A40U 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
D16V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATM MUTATED                                  0     0
  ATM WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED                           0    16
  ATM WILD-TYPE                        65   553
D16V12, multiclass
                                  clus
vv                                 ATM MUTATED ATM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  0            65
  WHITE                                     16           553
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
               cls
clus              0   1
  ATM MUTATED     1   9
  ATM WILD-TYPE  31 432
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    9
  ATM WILD-TYPE   31  432
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            31
  NOT HISPANIC OR LATINO           9           432
[1] 2 2
[1] FALSE

Clustering(17) Variable = ZNF814 MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2                0   1
  ZNF814 MUTATED    12   1
  ZNF814 WILD-TYPE 474 174
  ZNF814 MUTATED ZNF814 WILD-TYPE 
              13              648 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               1              174 
$`ZNF814 MUTATED`
TCGA-KL-8333 TCGA-KL-8344 TCGA-KO-8414 TCGA-BP-5196 TCGA-CJ-5675 TCGA-A4-A5Y1 
       98.33        28.80        77.85        33.47        79.89        12.99 
TCGA-B9-A44B TCGA-DW-7840 TCGA-G7-A4TM TCGA-GL-A4EM TCGA-IZ-8195 TCGA-KV-A6GE 
        2.10         3.75         6.38         1.05        22.26        29.10 
TCGA-P4-A5EB 
       84.95 

$`ZNF814 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       73.91        71.41        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78       103.27        86.10        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 
       61.58        63.95        39.16        49.08        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       60.92        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       23.47        13.41        24.62        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
       26.40        20.61         0.46        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       25.15        13.68        25.84       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
       27.65        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A55W 
       21.34        16.34        12.36         0.13        11.97        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       42.94         6.61        92.58        12.85        17.75        14.07 

  ZNF814 MUTATED ZNF814 WILD-TYPE 
            1.05             0.07 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           98.33           194.79 
  ZNF814 MUTATED ZNF814 WILD-TYPE 
           28.80            34.44 
[1] "1.1 - 98.3 (28.8)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "3.3"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF814 MUTATED         6        4         3        0
  ZNF814 WILD-TYPE     321       75       162       86
D17V3, multiclass
           clus
vv          ZNF814 MUTATED ZNF814 WILD-TYPE
  STAGE I                6              321
  STAGE II               4               75
  STAGE III              3              162
  STAGE IV               0               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
  ZNF814 MUTATED     7   4   2   0
  ZNF814 WILD-TYPE 333  93 219  10
D17V4, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  T1              7              333
  T2              4               93
  T3              2              219
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF814 MUTATED     3   1   0
  ZNF814 WILD-TYPE 269  35   6
D17V5, multiclass
    clus
vv   ZNF814 MUTATED ZNF814 WILD-TYPE
  N0              3              269
  N1              1               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     5   0
  ZNF814 WILD-TYPE 463  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      5    0
  ZNF814 WILD-TYPE  463   78
   clus
vv  ZNF814 MUTATED ZNF814 WILD-TYPE
  0              5              463
  1              0               78
[1] 2 2
[1] FALSE
D17V7, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     1  12
  ZNF814 WILD-TYPE 228 427
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      1   12
  ZNF814 WILD-TYPE  228  427
        clus
vv       ZNF814 MUTATED ZNF814 WILD-TYPE
  FEMALE              1              228
  MALE               12              427
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               77 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       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-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982       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-EU-5904       TCGA-EU-5905 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EU-5907       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7834       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-DW-7963       TCGA-EV-5901 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZNF814 MUTATED                    3                                 2
  ZNF814 WILD-TYPE                 63                               439
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZNF814 MUTATED                                       8
  ZNF814 WILD-TYPE                                   153
D17V9, multiclass
                                       clus
vv                                      ZNF814 MUTATED ZNF814 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 3               63
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              8              153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
[1] "Remove cluster labels:" "ZNF814 MUTATED"        
clus
  ZNF814 MUTATED ZNF814 WILD-TYPE 
               2               40 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-B8-4621 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A48D 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" "ZNF814 WILD-TYPE" 
D17V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF814 MUTATED                                  0     0
  ZNF814 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF814 MUTATED                           3    10
  ZNF814 WILD-TYPE                        62   559
D17V12, multiclass
                                  clus
vv                                 ZNF814 MUTATED ZNF814 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               62
  WHITE                                        10              559
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                  cls
clus                 0   1
  ZNF814 MUTATED     0  10
  ZNF814 WILD-TYPE  32 431
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF814 MUTATED      0   10
  ZNF814 WILD-TYPE   32  431
                        clus
vv                       ZNF814 MUTATED ZNF814 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO             10              431
[1] 2 2
[1] FALSE

Clustering(18) Variable = DNMT3A MUTATION ANALYSIS
D18V1, survival
                  sevent
clus2                0   1
  DNMT3A MUTATED    10   0
  DNMT3A WILD-TYPE 476 175
  DNMT3A MUTATED DNMT3A WILD-TYPE 
              10              651 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               0              175 
$`DNMT3A MUTATED`
TCGA-B0-5120 TCGA-B0-5697 TCGA-B4-5836 TCGA-BP-4160 TCGA-BP-4999 TCGA-BP-5181 
       16.21        60.33         4.64        94.72        41.62        49.15 
TCGA-BQ-5884 TCGA-GL-A59T TCGA-IA-A40Y TCGA-MH-A55Z 
       26.04        17.95         2.04        27.78 

$`DNMT3A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60        17.59         1.94        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       56.78        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.23         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        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       85.51        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-HE-A5NF 
       12.92         3.68        27.65         1.05        12.43        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       19.99        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.97        29.10        34.29        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  DNMT3A MUTATED DNMT3A WILD-TYPE 
            2.04             0.07 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           94.72           194.79 
  DNMT3A MUTATED DNMT3A WILD-TYPE 
           26.91            34.36 
[1] "2.0 - 94.7 (26.9)"  "0.1 - 194.8 (34.4)"
[1] "hr="     "9100000"
D18V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  DNMT3A MUTATED         8        0         2        0
  DNMT3A WILD-TYPE     319       79       163       86
D18V3, multiclass
           clus
vv          DNMT3A MUTATED DNMT3A WILD-TYPE
  STAGE I                8              319
  STAGE II               0               79
  STAGE III              2              163
  STAGE IV               0               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
  DNMT3A MUTATED     8   0   2   0
  DNMT3A WILD-TYPE 332  97 219  10
D18V4, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  T1              8              332
  T2              0               97
  T3              2              219
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  DNMT3A MUTATED     4   1   0
  DNMT3A WILD-TYPE 268  35   6
D18V5, multiclass
    clus
vv   DNMT3A MUTATED DNMT3A WILD-TYPE
  N0              4              268
  N1              1               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     7   0
  DNMT3A WILD-TYPE 461  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      7    0
  DNMT3A WILD-TYPE  461   78
   clus
vv  DNMT3A MUTATED DNMT3A WILD-TYPE
  0              7              461
  1              0               78
[1] 2 2
[1] FALSE
D18V7, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     5   5
  DNMT3A WILD-TYPE 224 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      5    5
  DNMT3A WILD-TYPE  224  434
        clus
vv       DNMT3A MUTATED DNMT3A WILD-TYPE
  FEMALE              5              224
  MALE                5              434
[1] 2 2
[1] FALSE
D18V8, continuous
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               2               77 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5465 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-J7-8537 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-Q2-A5QZ 
"DNMT3A WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  DNMT3A MUTATED                    0                                 6
  DNMT3A WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DNMT3A MUTATED                                       4
  DNMT3A WILD-TYPE                                   157
D18V9, multiclass
                                       clus
vv                                      DNMT3A MUTATED DNMT3A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
[1] "Remove cluster labels:" "DNMT3A MUTATED"        
clus
  DNMT3A MUTATED DNMT3A WILD-TYPE 
               1               41 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-B8-4621 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A48D 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9 
"DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" "DNMT3A WILD-TYPE" 
      TCGA-Q2-A5QZ 
"DNMT3A WILD-TYPE" 
D18V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DNMT3A MUTATED                                  0     0
  DNMT3A WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  DNMT3A MUTATED                           2     8
  DNMT3A WILD-TYPE                        63   561
D18V12, multiclass
                                  clus
vv                                 DNMT3A MUTATED DNMT3A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               63
  WHITE                                         8              561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                  cls
clus                 0   1
  DNMT3A MUTATED     1   7
  DNMT3A WILD-TYPE  31 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3A MUTATED      1    7
  DNMT3A WILD-TYPE   31  434
                        clus
vv                       DNMT3A MUTATED DNMT3A WILD-TYPE
  HISPANIC OR LATINO                  1               31
  NOT HISPANIC OR LATINO              7              434
[1] 2 2
[1] FALSE

Clustering(19) Variable = CDK12 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     6   3
  CDK12 WILD-TYPE 480 172
  CDK12 MUTATED CDK12 WILD-TYPE 
              9             652 
  CDK12 MUTATED CDK12 WILD-TYPE 
              3             172 
$`CDK12 MUTATED`
TCGA-KL-8327 TCGA-A3-3322 TCGA-B0-5098 TCGA-B0-5693 TCGA-B0-5706 TCGA-CJ-4881 
      137.06        48.59        52.08       101.13        79.36        66.21 
TCGA-CZ-5454 TCGA-CZ-5468 TCGA-DW-5560 
       23.74         1.94        11.61 

$`CDK12 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       49.02        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
       48.89        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5707 
       90.12        56.94        52.77        39.55       120.59        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.53        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        64.27        71.87        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 
       61.41        63.42        58.82         0.82        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        47.54        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 
       11.28         7.63         7.04         7.17         3.81        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  CDK12 MUTATED CDK12 WILD-TYPE 
           1.94            0.07 
  CDK12 MUTATED CDK12 WILD-TYPE 
         137.06          194.79 
  CDK12 MUTATED CDK12 WILD-TYPE 
          52.08           34.09 
[1] "1.9 - 137.1 (52.1)" "0.1 - 194.8 (34.1)"
[1] "hr=" "1.1"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CDK12 MUTATED         5        1         1        2
  CDK12 WILD-TYPE     322       78       164       84
D19V3, multiclass
           clus
vv          CDK12 MUTATED CDK12 WILD-TYPE
  STAGE I               5             322
  STAGE II              1              78
  STAGE III             1             164
  STAGE IV              2              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  CDK12 MUTATED     5   2   2   0
  CDK12 WILD-TYPE 335  95 219  10
D19V4, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T1             5             335
  T2             2              95
  T3             2             219
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  CDK12 MUTATED     3   0   0
  CDK12 WILD-TYPE 269  36   6
D19V5, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  N0             3             269
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                 cls
clus                0   1
  CDK12 MUTATED     7   2
  CDK12 WILD-TYPE 461  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      7    2
  CDK12 WILD-TYPE  461   76
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0             7             461
  1             2              76
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  CDK12 MUTATED     4   5
  CDK12 WILD-TYPE 225 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      4    5
  CDK12 WILD-TYPE  225  434
        clus
vv       CDK12 MUTATED CDK12 WILD-TYPE
  FEMALE             4             225
  MALE               5             434
[1] 2 2
[1] FALSE
D19V8, continuous
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      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-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      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-EU-5904      TCGA-EU-5905 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5561      TCGA-DW-7834 
"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-DW-7963      TCGA-EV-5901 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CDK12 MUTATED                    1                                 7
  CDK12 WILD-TYPE                 65                               434
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CDK12 MUTATED                                       1
  CDK12 WILD-TYPE                                   160
D19V9, multiclass
                                       clus
vv                                      CDK12 MUTATED CDK12 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 7             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CDK12 MUTATED                                  0     0
  CDK12 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED                           1     8
  CDK12 WILD-TYPE                        64   561
D19V12, multiclass
                                  clus
vv                                 CDK12 MUTATED CDK12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        8             561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                 cls
clus                0   1
  CDK12 MUTATED     0   7
  CDK12 WILD-TYPE  32 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      0    7
  CDK12 WILD-TYPE   32  434
                        clus
vv                       CDK12 MUTATED CDK12 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             7             434
[1] 2 2
[1] FALSE

Clustering(20) Variable = CSGALNACT2 MUTATION ANALYSIS
D20V1, survival
                      sevent
clus2                    0   1
  CSGALNACT2 MUTATED     7   0
  CSGALNACT2 WILD-TYPE 479 175
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   7                  654 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   0                  175 
$`CSGALNACT2 MUTATED`
TCGA-KL-8329 TCGA-KL-8334 TCGA-CZ-5984 TCGA-A4-A4ZT TCGA-HE-A5NK TCGA-KV-A6GD 
       90.48        96.95        67.96        16.96        73.25        11.97 
TCGA-MH-A560 
       30.38 

$`CSGALNACT2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        98.33        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       56.75         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-MH-A55W 
       21.34        16.34        12.36         0.13        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.78        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               11.97                 0.07 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               96.95               194.79 
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
               67.96                34.24 
[1] "12.0 - 97.0 (68.0)" "0.1 - 194.8 (34.2)"
[1] "hr="     "9100000"
D20V2, continuous
                      vv
clus                   STAGE I STAGE II STAGE III STAGE IV
  CSGALNACT2 MUTATED         5        0         2        0
  CSGALNACT2 WILD-TYPE     322       79       163       86
D20V3, multiclass
           clus
vv          CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  STAGE I                    5                  322
  STAGE II                   0                   79
  STAGE III                  2                  163
  STAGE IV                   0                   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
  CSGALNACT2 MUTATED     6   0   2   0
  CSGALNACT2 WILD-TYPE 334  97 219  10
D20V4, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  T1                  6                  334
  T2                  0                   97
  T3                  2                  219
  T4                  0                   10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                      vv
clus                    N0  N1  N2
  CSGALNACT2 MUTATED     3   0   0
  CSGALNACT2 WILD-TYPE 269  36   6
D20V5, multiclass
    clus
vv   CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  N0                  3                  269
  N1                  0                   36
  N2                  0                    6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     6   0
  CSGALNACT2 WILD-TYPE 462  78
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      6    0
  CSGALNACT2 WILD-TYPE  462   78
   clus
vv  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  0                  6                  462
  1                  0                   78
[1] 2 2
[1] FALSE
D20V7, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     4   4
  CSGALNACT2 WILD-TYPE 225 435
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      4    4
  CSGALNACT2 WILD-TYPE  225  435
        clus
vv       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  FEMALE                  4                  225
  MALE                    4                  435
[1] 2 2
[1] FALSE
D20V8, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   78 
          TCGA-KM-8438           TCGA-KM-8439           TCGA-KM-8440 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KM-8441           TCGA-KM-8442           TCGA-KM-8443 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KM-8476           TCGA-KM-8477           TCGA-KM-8639 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KO-8411           TCGA-KO-8413           TCGA-AK-3430 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B0-4838           TCGA-B4-5377           TCGA-B4-5832 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B4-5834           TCGA-B4-5835           TCGA-B4-5836 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B4-5838           TCGA-B4-5843           TCGA-B4-5844 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-4854           TCGA-CZ-4856           TCGA-CZ-4858 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-4861           TCGA-CZ-4862           TCGA-CZ-5456 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-5457           TCGA-CZ-5465           TCGA-CZ-5469 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-CZ-5982           TCGA-DV-5565           TCGA-DV-5566 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DV-5568           TCGA-DV-5569           TCGA-DV-5574 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DV-5575           TCGA-DV-5576           TCGA-EU-5904 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EU-5905           TCGA-EU-5907           TCGA-A4-7286 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-7828           TCGA-A4-8310           TCGA-A4-8311 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-8312           TCGA-A4-8518           TCGA-A4-8630 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A57E           TCGA-A4-A5DU           TCGA-A4-A5XZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A6HP           TCGA-AL-3466           TCGA-DW-5560 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-5561           TCGA-DW-7834           TCGA-DW-7837 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7838           TCGA-DW-7839           TCGA-DW-7840 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-7841           TCGA-DW-7842           TCGA-DW-7963 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-EV-5901           TCGA-EV-5902           TCGA-EV-5903 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6790           TCGA-G7-6793           TCGA-G7-6796 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-6797           TCGA-G7-7501           TCGA-G7-7502 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-A4TM           TCGA-IA-A40U           TCGA-IA-A40X 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IA-A40Y           TCGA-J7-8537           TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
                      vv
clus                   KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CSGALNACT2 MUTATED                    2                                 1
  CSGALNACT2 WILD-TYPE                 64                               440
                      vv
clus                   KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CSGALNACT2 MUTATED                                       5
  CSGALNACT2 WILD-TYPE                                   156
D20V9, multiclass
                                       clus
vv                                      CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                     2                   64
  KIDNEY CLEAR CELL RENAL CARCINOMA                      1                  440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                  5                  156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
[1] "Remove cluster labels:" "CSGALNACT2 MUTATED"    
clus
  CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE 
                   1                   41 
          TCGA-KL-8324           TCGA-KL-8330           TCGA-KL-8335 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KL-8341           TCGA-KL-8345           TCGA-KM-8639 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KN-8428           TCGA-KN-8433           TCGA-KO-8408 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-KO-8409           TCGA-KO-8416           TCGA-B8-4621 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B8-5158           TCGA-B8-5164           TCGA-A4-8310 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-A4-A48D           TCGA-A4-A57E           TCGA-A4-A5Y0 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-AL-3466           TCGA-AL-3472           TCGA-AL-7173 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B1-A654           TCGA-B9-4115           TCGA-B9-4117 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-B9-7268           TCGA-B9-A44B           TCGA-B9-A69E 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-DW-5561           TCGA-DW-7834           TCGA-DW-7963 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-G7-7501           TCGA-GL-7773           TCGA-GL-A59T 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-HE-A5NI           TCGA-HE-A5NJ           TCGA-IA-A40U 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-IZ-A6M8           TCGA-P4-A5E7           TCGA-P4-A5EB 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
          TCGA-PJ-A5Z9           TCGA-Q2-A5QZ 
"CSGALNACT2 WILD-TYPE" "CSGALNACT2 WILD-TYPE" 
D20V11, continuous
                      vv
clus                   AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSGALNACT2 MUTATED                                  0     1
  CSGALNACT2 WILD-TYPE                                2    10
                      vv
clus                   BLACK OR AFRICAN AMERICAN WHITE
  CSGALNACT2 MUTATED                           0     5
  CSGALNACT2 WILD-TYPE                        65   564
D20V12, multiclass
                                  clus
vv                                 CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                  0                    2
  ASIAN                                             1                   10
  BLACK OR AFRICAN AMERICAN                         0                   65
  WHITE                                             5                  564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                      cls
clus                     0   1
  CSGALNACT2 MUTATED     0   3
  CSGALNACT2 WILD-TYPE  32 438
[1] "tbl2"
                      cls
clus                   [,1] [,2]
  CSGALNACT2 MUTATED      0    3
  CSGALNACT2 WILD-TYPE   32  438
                        clus
vv                       CSGALNACT2 MUTATED CSGALNACT2 WILD-TYPE
  HISPANIC OR LATINO                      0                   32
  NOT HISPANIC OR LATINO                  3                  438
[1] 2 2
[1] FALSE

Clustering(21) Variable = PIK3CA MUTATION ANALYSIS
D21V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     9   5
  PIK3CA WILD-TYPE 477 170
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              14              647 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5              170 
$`PIK3CA MUTATED`
TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-4824 TCGA-B0-5713 TCGA-B8-5159 TCGA-BP-4160 
       88.37         2.53        54.48        61.32        23.74        94.72 
TCGA-BP-4352 TCGA-BP-4960 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 
       11.31        71.41        47.18        74.27        64.18         7.36 
TCGA-BQ-5893 TCGA-DZ-6134 
        7.92        61.02 

$`PIK3CA WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       52.93        45.53        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         1.41         4.57         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       36.53        14.93        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        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 
       25.55        25.91        23.01        20.91         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 
        0.53        34.39        14.30       111.02        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        31.89        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.71        47.97         6.94        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        69.86        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66        83.77        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           94.72           194.79 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           57.75            33.99 
[1] "2.5 - 94.7 (57.8)"  "0.1 - 194.8 (34.0)"
[1] "hr=" "1.1"
D21V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         5        2         4        3
  PIK3CA WILD-TYPE     322       77       161       83
D21V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                5              322
  STAGE II               2               77
  STAGE III              4              161
  STAGE IV               3               83
[1] 4 2
[1] 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     5   2   7   0
  PIK3CA WILD-TYPE 335  95 214  10
D21V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              5              335
  T2              2               95
  T3              7              214
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  PIK3CA MUTATED    11   1   0
  PIK3CA WILD-TYPE 261  35   6
D21V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             11              261
  N1              1               35
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10   3
  PIK3CA WILD-TYPE 458  75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    3
  PIK3CA WILD-TYPE  458   75
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             10              458
  1              3               75
[1] 2 2
[1] FALSE
D21V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   6
  PIK3CA WILD-TYPE 221 433
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    6
  PIK3CA WILD-TYPE  221  433
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              8              221
  MALE                6              433
[1] 2 2
[1] FALSE
D21V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PIK3CA MUTATED                    0                                12
  PIK3CA WILD-TYPE                 66                               429
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PIK3CA MUTATED                                       2
  PIK3CA WILD-TYPE                                   159
D21V9, multiclass
                                       clus
vv                                      PIK3CA MUTATED PIK3CA WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 12              429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PIK3CA MUTATED                                  0     0
  PIK3CA WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED                           0    14
  PIK3CA WILD-TYPE                        65   555
D21V12, multiclass
                                  clus
vv                                 PIK3CA MUTATED PIK3CA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                        14              555
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  11
  PIK3CA WILD-TYPE  31 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   11
  PIK3CA WILD-TYPE   31  430
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               31
  NOT HISPANIC OR LATINO             11              430
[1] 2 2
[1] FALSE

Clustering(22) Variable = KIAA1751 MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  KIAA1751 MUTATED     6   2
  KIAA1751 WILD-TYPE 480 173
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 8                653 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 2                173 
$`KIAA1751 MUTATED`
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3434 TCGA-B0-5703 TCGA-CZ-5467 TCGA-CZ-5984 
       73.08        15.78        68.61        39.55         2.40        67.96 
TCGA-A4-A4ZT TCGA-DW-7840 
       16.96         3.75 

$`KIAA1751 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       66.31        60.92        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 
       84.92        90.12        56.94        52.77       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       92.98       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        31.10        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
              2.40               0.07 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
             73.08             194.79 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
            28.255             34.290 
[1] "2.4 - 73.1 (28.3)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1751 MUTATED         5        0         3        0
  KIAA1751 WILD-TYPE     322       79       162       86
D22V3, multiclass
           clus
vv          KIAA1751 MUTATED KIAA1751 WILD-TYPE
  STAGE I                  5                322
  STAGE II                 0                 79
  STAGE III                3                162
  STAGE IV                 0                 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
  KIAA1751 MUTATED     5   0   3   0
  KIAA1751 WILD-TYPE 335  97 218  10
D22V4, multiclass
    clus
vv   KIAA1751 MUTATED KIAA1751 WILD-TYPE
  T1                5                335
  T2                0                 97
  T3                3                218
  T4                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  KIAA1751 MUTATED     4   1   0
  KIAA1751 WILD-TYPE 268  35   6
D22V5, multiclass
    clus
vv   KIAA1751 MUTATED KIAA1751 WILD-TYPE
  N0                4                268
  N1                1                 35
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     6   0
  KIAA1751 WILD-TYPE 462  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      6    0
  KIAA1751 WILD-TYPE  462   78
   clus
vv  KIAA1751 MUTATED KIAA1751 WILD-TYPE
  0                6                462
  1                0                 78
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     2   6
  KIAA1751 WILD-TYPE 227 433
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      2    6
  KIAA1751 WILD-TYPE  227  433
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  FEMALE                2                227
  MALE                  6                433
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  KIAA1751 MUTATED                    0                                 6
  KIAA1751 WILD-TYPE                 66                               435
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  KIAA1751 MUTATED                                       2
  KIAA1751 WILD-TYPE                                   159
D22V9, multiclass
                                       clus
vv                                      KIAA1751 MUTATED KIAA1751 WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                    6                435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                2                159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIAA1751 MUTATED                                  0     0
  KIAA1751 WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  KIAA1751 MUTATED                           1     7
  KIAA1751 WILD-TYPE                        64   562
D22V12, multiclass
                                  clus
vv                                 KIAA1751 MUTATED KIAA1751 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       1                 64
  WHITE                                           7                562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     0   7
  KIAA1751 WILD-TYPE  32 434
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      0    7
  KIAA1751 WILD-TYPE   32  434
                        clus
vv                       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO                7                434
[1] 2 2
[1] FALSE

Clustering(23) Variable = MTOR MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    17  14
  MTOR WILD-TYPE 469 161
  MTOR MUTATED MTOR WILD-TYPE 
            31            630 
  MTOR MUTATED MTOR WILD-TYPE 
            14            161 
$`MTOR MUTATED`
TCGA-KM-8441 TCGA-KN-8437 TCGA-A3-3347 TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 
       28.80       100.87        52.93        66.31        15.72        29.10 
TCGA-B0-4846 TCGA-B0-4852 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5691 
       39.45        36.85        52.08        62.89         1.94       112.80 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5712 TCGA-B4-5832 TCGA-B4-5836 
       56.78        60.33        56.94        89.49         0.23         4.64 
TCGA-B4-5844 TCGA-BP-5175 TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4887 TCGA-CJ-4907 
        0.23        30.64        52.27        11.05        30.64        49.28 
TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5987 
       22.32        60.99        64.57        47.08        61.41        14.63 
TCGA-BQ-7061 
        7.17 

$`MTOR WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38        48.82        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
       20.28       109.91        84.36        73.08        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 
       68.61        67.20        57.37        46.78        42.08        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 
        4.57         2.53         3.48        19.00        65.10         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4847 
        6.71        56.68        11.64        10.29        65.29        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5102 
       10.95         8.05         2.24        21.86        15.95        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60        17.59        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       21.44        37.22        14.76        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       46.68        84.92        90.12        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       79.36        92.98       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5835 
       11.77        10.36        21.57         9.57         1.25         0.53 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        5.46         0.36        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 
       48.10         6.35        79.30         1.78        74.20         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        69.86        64.18        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        67.00        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
        7.36        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16         0.59        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       12.26        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       49.84        26.27        11.28         7.63         7.04         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  MTOR MUTATED MTOR WILD-TYPE 
          0.23           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        112.80         194.79 
  MTOR MUTATED MTOR WILD-TYPE 
         47.08          33.91 
[1] "0.2 - 112.8 (47.1)" "0.1 - 194.8 (33.9)"
[1] "hr=" "1.6"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED        12        4         9        7
  MTOR WILD-TYPE     315       75       156       79
D23V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I             12            315
  STAGE II             4             75
  STAGE III            9            156
  STAGE IV             7             79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  MTOR MUTATED    14   4  14   0
  MTOR WILD-TYPE 326  93 207  10
D23V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1           14            326
  T2            4             93
  T3           14            207
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  MTOR MUTATED    15   2   0
  MTOR WILD-TYPE 257  34   6
D23V5, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  N0           15            257
  N1            2             34
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                cls
clus               0   1
  MTOR MUTATED    23   7
  MTOR WILD-TYPE 445  71
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     23    7
  MTOR WILD-TYPE  445   71
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           23            445
  1            7             71
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  MTOR MUTATED    18  14
  MTOR WILD-TYPE 211 425
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     18   14
  MTOR WILD-TYPE  211  425
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           18            211
  MALE             14            425
[1] 2 2
[1] FALSE
D23V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MTOR MUTATED                    2                                28
  MTOR WILD-TYPE                 64                               413
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MTOR MUTATED                                       2
  MTOR WILD-TYPE                                   159
D23V9, multiclass
                                       clus
vv                                      MTOR MUTATED MTOR WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA               28            413
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
D23V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MTOR MUTATED                                  0     0
  MTOR WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED                           4    28
  MTOR WILD-TYPE                        61   541
D23V12, multiclass
                                  clus
vv                                 MTOR MUTATED MTOR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   4             61
  WHITE                                      28            541
[1] 4 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
  MTOR MUTATED     1  29
  MTOR WILD-TYPE  31 412
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   29
  MTOR WILD-TYPE   31  412
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             31
  NOT HISPANIC OR LATINO           29            412
[1] 2 2
[1] FALSE

Clustering(24) Variable = RIMBP3 MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  RIMBP3 MUTATED     2   3
  RIMBP3 WILD-TYPE 484 172
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               5              656 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               3              172 
$`RIMBP3 MUTATED`
TCGA-KO-8404 TCGA-KO-8409 TCGA-B0-4945 TCGA-BP-4164 TCGA-BP-4964 
       10.68        80.38        70.52        32.61        61.22 

$`RIMBP3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
        2.27        36.85        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           10.68             0.07 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           80.38           194.79 
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
           61.22            34.24 
[1] "10.7 - 80.4 (61.2)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.7"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RIMBP3 MUTATED         2        1         1        1
  RIMBP3 WILD-TYPE     325       78       164       85
D24V3, multiclass
           clus
vv          RIMBP3 MUTATED RIMBP3 WILD-TYPE
  STAGE I                2              325
  STAGE II               1               78
  STAGE III              1              164
  STAGE IV               1               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
  RIMBP3 MUTATED     2   1   1   1
  RIMBP3 WILD-TYPE 338  96 220   9
D24V4, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  T1              2              338
  T2              1               96
  T3              1              220
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RIMBP3 MUTATED     3   0   0
  RIMBP3 WILD-TYPE 269  36   6
D24V5, multiclass
    clus
vv   RIMBP3 MUTATED RIMBP3 WILD-TYPE
  N0              3              269
  N1              0               36
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     4   0
  RIMBP3 WILD-TYPE 464  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      4    0
  RIMBP3 WILD-TYPE  464   78
   clus
vv  RIMBP3 MUTATED RIMBP3 WILD-TYPE
  0              4              464
  1              0               78
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     3   2
  RIMBP3 WILD-TYPE 226 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      3    2
  RIMBP3 WILD-TYPE  226  437
        clus
vv       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  FEMALE              3              226
  MALE                2              437
[1] 2 2
[1] FALSE
D24V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RIMBP3 MUTATED                    2                                 3
  RIMBP3 WILD-TYPE                 64                               438
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RIMBP3 MUTATED                                       0
  RIMBP3 WILD-TYPE                                   161
D24V9, multiclass
                                       clus
vv                                      RIMBP3 MUTATED RIMBP3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  3              438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              0              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               41 
      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-B8-4621       TCGA-B8-5158 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B8-5164       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-B9-4115       TCGA-B9-4117       TCGA-B9-7268 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" 
D24V11, continuous
[1] "Remove cluster labels:" "RIMBP3 MUTATED"        
clus
  RIMBP3 MUTATED RIMBP3 WILD-TYPE 
               1               25 
      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-B8-5158 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4117       TCGA-B9-A69E 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-IA-A40U       TCGA-P4-A5E6       TCGA-PJ-A5Z9 
"RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" "RIMBP3 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"RIMBP3 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RIMBP3 MUTATED                                  0     0
  RIMBP3 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RIMBP3 MUTATED                           0     5
  RIMBP3 WILD-TYPE                        65   564
D24V12, multiclass
                                  clus
vv                                 RIMBP3 MUTATED RIMBP3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         5              564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                  cls
clus                 0   1
  RIMBP3 MUTATED     0   3
  RIMBP3 WILD-TYPE  32 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RIMBP3 MUTATED      0    3
  RIMBP3 WILD-TYPE   32  438
                        clus
vv                       RIMBP3 MUTATED RIMBP3 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              3              438
[1] 2 2
[1] FALSE

Clustering(25) Variable = ZNF598 MUTATION ANALYSIS
D25V1, survival
                  sevent
clus2                0   1
  ZNF598 MUTATED     8   2
  ZNF598 WILD-TYPE 478 173
  ZNF598 MUTATED ZNF598 WILD-TYPE 
              10              651 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               2              173 
$`ZNF598 MUTATED`
TCGA-AL-3473 TCGA-AT-A5NU TCGA-B3-8121 TCGA-BQ-5877 TCGA-BQ-5893 TCGA-DW-7834 
       25.08         2.20        12.46         8.88         7.92       129.86 
TCGA-DW-7838 TCGA-EV-5903 TCGA-G7-7501 TCGA-G7-7502 
       24.46        24.89        13.68        25.84 

$`ZNF598 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       30.35        44.61        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       14.86        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-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.17         3.81        11.61        13.61        37.55        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ 
       51.19        61.02        54.90        34.19        19.00        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.15         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  ZNF598 MUTATED ZNF598 WILD-TYPE 
            2.20             0.07 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
          129.86           194.79 
  ZNF598 MUTATED ZNF598 WILD-TYPE 
           19.07            34.82 
[1] "2.2 - 129.9 (19.1)" "0.1 - 194.8 (34.8)"
[1] "hr=" "1.3"
D25V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF598 MUTATED         7        1         1        2
  ZNF598 WILD-TYPE     320       78       164       84
D25V3, multiclass
           clus
vv          ZNF598 MUTATED ZNF598 WILD-TYPE
  STAGE I                7              320
  STAGE II               1               78
  STAGE III              1              164
  STAGE IV               2               84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  ZNF598 MUTATED     7   1   3   0
  ZNF598 WILD-TYPE 333  96 218  10
D25V4, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  T1              7              333
  T2              1               96
  T3              3              218
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZNF598 MUTATED     2   3   0
  ZNF598 WILD-TYPE 270  33   6
D25V5, multiclass
    clus
vv   ZNF598 MUTATED ZNF598 WILD-TYPE
  N0              2              270
  N1              3               33
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   2
  ZNF598 WILD-TYPE 466  76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    2
  ZNF598 WILD-TYPE  466   76
   clus
vv  ZNF598 MUTATED ZNF598 WILD-TYPE
  0              2              466
  1              2               76
[1] 2 2
[1] FALSE
D25V7, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     2   9
  ZNF598 WILD-TYPE 227 430
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      2    9
  ZNF598 WILD-TYPE  227  430
        clus
vv       ZNF598 MUTATED ZNF598 WILD-TYPE
  FEMALE              2              227
  MALE                9              430
[1] 2 2
[1] FALSE
D25V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZNF598 MUTATED                    1                                 0
  ZNF598 WILD-TYPE                 65                               441
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZNF598 MUTATED                                      10
  ZNF598 WILD-TYPE                                   151
D25V9, multiclass
                                       clus
vv                                      ZNF598 MUTATED ZNF598 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  0              441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             10              151
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
[1] "Remove cluster labels:" "ZNF598 MUTATED"        
clus
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               2               40 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-B8-4621 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A48D 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-DW-7963       TCGA-GL-7773       TCGA-GL-A59T       TCGA-HE-A5NI 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
D25V11, continuous
[1] "Remove cluster labels:" "ZNF598 MUTATED"        
clus
  ZNF598 MUTATED ZNF598 WILD-TYPE 
               1               25 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B8-5158       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4117 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7963       TCGA-GL-7773 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-IA-A40U       TCGA-P4-A5E6       TCGA-PJ-A5Z9 
"ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" "ZNF598 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"ZNF598 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZNF598 MUTATED                                  0     0
  ZNF598 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZNF598 MUTATED                           3     8
  ZNF598 WILD-TYPE                        62   561
D25V12, multiclass
                                  clus
vv                                 ZNF598 MUTATED ZNF598 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     3               62
  WHITE                                         8              561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                  cls
clus                 0   1
  ZNF598 MUTATED     1   9
  ZNF598 WILD-TYPE  31 432
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF598 MUTATED      1    9
  ZNF598 WILD-TYPE   31  432
                        clus
vv                       ZNF598 MUTATED ZNF598 WILD-TYPE
  HISPANIC OR LATINO                  1               31
  NOT HISPANIC OR LATINO              9              432
[1] 2 2
[1] FALSE

Clustering(26) Variable = GPR50 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 483 173
  GPR50 MUTATED GPR50 WILD-TYPE 
              5             656 
  GPR50 MUTATED GPR50 WILD-TYPE 
              2             173 
$`GPR50 MUTATED`
TCGA-KN-8436 TCGA-B0-4817 TCGA-DV-5575 TCGA-DV-5576 TCGA-PJ-A5Z9 
       42.35        33.50        56.84        23.90        17.75 

$`GPR50 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        52.21        45.07        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       12.85        14.07 

  GPR50 MUTATED GPR50 WILD-TYPE 
          17.75            0.07 
  GPR50 MUTATED GPR50 WILD-TYPE 
          56.84          194.79 
  GPR50 MUTATED GPR50 WILD-TYPE 
         33.500          34.325 
[1] "17.8 - 56.8 (33.5)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.7"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  GPR50 MUTATED         3        1         1        0
  GPR50 WILD-TYPE     324       78       164       86
D26V3, multiclass
           clus
vv          GPR50 MUTATED GPR50 WILD-TYPE
  STAGE I               3             324
  STAGE II              1              78
  STAGE III             1             164
  STAGE IV              0              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
  GPR50 MUTATED     3   1   1   0
  GPR50 WILD-TYPE 337  96 220  10
D26V4, multiclass
    clus
vv   GPR50 MUTATED GPR50 WILD-TYPE
  T1             3             337
  T2             1              96
  T3             1             220
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  GPR50 MUTATED     1   0   0
  GPR50 WILD-TYPE 271  36   6
D26V5, multiclass
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4833 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839      TCGA-B0-4842 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852      TCGA-B0-4945 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-4621      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-4158      TCGA-BP-4159      TCGA-BP-4160 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"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-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4856      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-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B1-A657      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-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-P4-A5EA 
"GPR50 WILD-TYPE" 
D26V6, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   0
  GPR50 WILD-TYPE 465  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    0
  GPR50 WILD-TYPE  465   78
   clus
vv  GPR50 MUTATED GPR50 WILD-TYPE
  0             3             465
  1             0              78
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  GPR50 MUTATED     3   2
  GPR50 WILD-TYPE 226 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      3    2
  GPR50 WILD-TYPE  226  437
        clus
vv       GPR50 MUTATED GPR50 WILD-TYPE
  FEMALE             3             226
  MALE               2             437
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              2              77 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      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-EU-5904      TCGA-EU-5905      TCGA-EU-5907      TCGA-A4-7286 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311      TCGA-A4-8312 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT      TCGA-A4-A57E 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP      TCGA-AL-3466 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      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-DW-7963      TCGA-EV-5901      TCGA-EV-5902 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6796 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GPR50 MUTATED                    1                                 3
  GPR50 WILD-TYPE                 65                               438
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GPR50 MUTATED                                       1
  GPR50 WILD-TYPE                                   160
D26V9, multiclass
                                       clus
vv                                      GPR50 MUTATED GPR50 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              41 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5158      TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-A59T      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-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" 
D26V11, continuous
[1] "Remove cluster labels:" "GPR50 MUTATED"         
clus
  GPR50 MUTATED GPR50 WILD-TYPE 
              1              25 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B8-5158      TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6 
"GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" "GPR50 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"GPR50 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR50 MUTATED                                  0     0
  GPR50 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  GPR50 MUTATED                           1     4
  GPR50 WILD-TYPE                        64   565
D26V12, multiclass
                                  clus
vv                                 GPR50 MUTATED GPR50 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        4             565
[1] 4 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
  GPR50 MUTATED     0   5
  GPR50 WILD-TYPE  32 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  GPR50 MUTATED      0    5
  GPR50 WILD-TYPE   32  436
                        clus
vv                       GPR50 MUTATED GPR50 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(27) Variable = CCDC120 MUTATION ANALYSIS
D27V1, survival
                   sevent
clus2                 0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 482 175
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               657 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                0               175 
$`CCDC120 MUTATED`
TCGA-AK-3425 TCGA-BP-4759 TCGA-CJ-4876 TCGA-CZ-5470 
      109.91        77.98        64.27        12.69 

$`CCDC120 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 
       18.64        28.31        65.52        20.28        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06        77.36        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        31.10        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  CCDC120 MUTATED CCDC120 WILD-TYPE 
            12.69              0.07 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           109.91            194.79 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           71.125            34.190 
[1] "12.7 - 109.9 (71.1)" "0.1 - 194.8 (34.2)" 
[1] "hr="     "3300000"
D27V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC120 MUTATED         2        2         0        0
  CCDC120 WILD-TYPE     325       77       165       86
D27V3, multiclass
           clus
vv          CCDC120 MUTATED CCDC120 WILD-TYPE
  STAGE I                 2               325
  STAGE II                2                77
  STAGE III               0               165
  STAGE IV                0                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
  CCDC120 MUTATED     2   2   0   0
  CCDC120 WILD-TYPE 338  95 221  10
D27V4, multiclass
    clus
vv   CCDC120 MUTATED CCDC120 WILD-TYPE
  T1               2               338
  T2               2                95
  T3               0               221
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CCDC120 MUTATED     3   0   0
  CCDC120 WILD-TYPE 269  36   6
D27V5, multiclass
    clus
vv   CCDC120 MUTATED CCDC120 WILD-TYPE
  N0               3               269
  N1               0                36
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 464  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      4    0
  CCDC120 WILD-TYPE  464   78
   clus
vv  CCDC120 MUTATED CCDC120 WILD-TYPE
  0               4               464
  1               0                78
[1] 2 2
[1] FALSE
D27V7, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     1   3
  CCDC120 WILD-TYPE 228 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    3
  CCDC120 WILD-TYPE  228  436
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  FEMALE               1               228
  MALE                 3               436
[1] 2 2
[1] FALSE
D27V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CCDC120 MUTATED                    0                                 4
  CCDC120 WILD-TYPE                 66                               437
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CCDC120 MUTATED                                       0
  CCDC120 WILD-TYPE                                   161
D27V9, multiclass
                                       clus
vv                                      CCDC120 MUTATED CCDC120 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   4               437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC120 MUTATED                                  0     0
  CCDC120 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CCDC120 MUTATED                           0     3
  CCDC120 WILD-TYPE                        65   566
D27V12, multiclass
                                  clus
vv                                 CCDC120 MUTATED CCDC120 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                65
  WHITE                                          3               566
[1] 4 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
  CCDC120 MUTATED     1   2
  CCDC120 WILD-TYPE  31 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    2
  CCDC120 WILD-TYPE   31  439
                        clus
vv                       CCDC120 MUTATED CCDC120 WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(28) Variable = SLC6A14 MUTATION ANALYSIS
D28V1, survival
                   sevent
clus2                 0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE 483 173
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                5               656 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2               173 
$`SLC6A14 MUTATED`
TCGA-KO-8416 TCGA-BP-4972 TCGA-BP-4985 TCGA-G7-6789 TCGA-P4-A5E7 
       61.58        49.38        31.30         4.01        87.22 

$`SLC6A14 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       86.10        77.85        57.17        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       48.89        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6790 
       54.90        34.19        19.00        24.89        10.68        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       99.78        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
             4.01              0.07 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
            87.22            194.79 
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
            49.38             34.24 
[1] "4.0 - 87.2 (49.4)"  "0.1 - 194.8 (34.2)"
[1] "hr=" "1.3"
D28V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC6A14 MUTATED         1        0         3        1
  SLC6A14 WILD-TYPE     326       79       162       85
D28V3, multiclass
           clus
vv          SLC6A14 MUTATED SLC6A14 WILD-TYPE
  STAGE I                 1               326
  STAGE II                0                79
  STAGE III               3               162
  STAGE IV                1                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
  SLC6A14 MUTATED     1   0   4   0
  SLC6A14 WILD-TYPE 339  97 217  10
D28V4, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  T1               1               339
  T2               0                97
  T3               4               217
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC6A14 MUTATED     2   0   1
  SLC6A14 WILD-TYPE 270  36   5
D28V5, multiclass
    clus
vv   SLC6A14 MUTATED SLC6A14 WILD-TYPE
  N0               2               270
  N1               0                36
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   0
  SLC6A14 WILD-TYPE 465  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    0
  SLC6A14 WILD-TYPE  465   78
   clus
vv  SLC6A14 MUTATED SLC6A14 WILD-TYPE
  0               3               465
  1               0                78
[1] 2 2
[1] FALSE
D28V7, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     3   2
  SLC6A14 WILD-TYPE 226 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      3    2
  SLC6A14 WILD-TYPE  226  437
        clus
vv       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  FEMALE               3               226
  MALE                 2               437
[1] 2 2
[1] FALSE
D28V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC6A14 MUTATED                    1                                 2
  SLC6A14 WILD-TYPE                 65                               439
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC6A14 MUTATED                                       2
  SLC6A14 WILD-TYPE                                   159
D28V9, multiclass
                                       clus
vv                                      SLC6A14 MUTATED SLC6A14 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
[1] "Remove cluster labels:" "SLC6A14 MUTATED"       
clus
  SLC6A14 MUTATED SLC6A14 WILD-TYPE 
                2                40 
       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-B8-4621        TCGA-B8-5158 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B8-5164        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-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-DW-7963        TCGA-G7-7501        TCGA-GL-7773        TCGA-GL-A59T 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-P4-A5EB        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" "SLC6A14 WILD-TYPE" 
D28V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC6A14 MUTATED                                  0     0
  SLC6A14 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC6A14 MUTATED                           0     5
  SLC6A14 WILD-TYPE                        65   564
D28V12, multiclass
                                  clus
vv                                 SLC6A14 MUTATED SLC6A14 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                65
  WHITE                                          5               564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                   cls
clus                  0   1
  SLC6A14 MUTATED     0   3
  SLC6A14 WILD-TYPE  32 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC6A14 MUTATED      0    3
  SLC6A14 WILD-TYPE   32  438
                        clus
vv                       SLC6A14 MUTATED SLC6A14 WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               3               438
[1] 2 2
[1] FALSE

Clustering(29) Variable = CYP4F11 MUTATION ANALYSIS
D29V1, survival
                   sevent
clus2                 0   1
  CYP4F11 MUTATED     4   1
  CYP4F11 WILD-TYPE 482 174
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                5               656 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                1               174 
$`CYP4F11 MUTATED`
TCGA-KN-8427 TCGA-AK-3428 TCGA-B4-5844 TCGA-BP-4338 TCGA-BP-4787 
        0.99        73.08         0.23        93.99        15.78 

$`CYP4F11 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        84.36        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       80.68         0.07        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       11.64        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
             0.23              0.07 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
            93.99            194.79 
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
           15.780            34.325 
[1] "0.2 - 94.0 (15.8)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "1.2"
D29V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CYP4F11 MUTATED         1        1         1        2
  CYP4F11 WILD-TYPE     326       78       164       84
D29V3, multiclass
           clus
vv          CYP4F11 MUTATED CYP4F11 WILD-TYPE
  STAGE I                 1               326
  STAGE II                1                78
  STAGE III               1               164
  STAGE IV                2                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  CYP4F11 MUTATED     1   1   2   1
  CYP4F11 WILD-TYPE 339  96 219   9
D29V4, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  T1               1               339
  T2               1                96
  T3               2               219
  T4               1                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  CYP4F11 MUTATED     4   1   0
  CYP4F11 WILD-TYPE 268  35   6
D29V5, multiclass
    clus
vv   CYP4F11 MUTATED CYP4F11 WILD-TYPE
  N0               4               268
  N1               1                35
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     3   1
  CYP4F11 WILD-TYPE 465  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      3    1
  CYP4F11 WILD-TYPE  465   77
   clus
vv  CYP4F11 MUTATED CYP4F11 WILD-TYPE
  0               3               465
  1               1                77
[1] 2 2
[1] FALSE
D29V7, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     2   3
  CYP4F11 WILD-TYPE 227 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      2    3
  CYP4F11 WILD-TYPE  227  436
        clus
vv       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  FEMALE               2               227
  MALE                 3               436
[1] 2 2
[1] FALSE
D29V8, continuous
[1] "Remove cluster labels:" "CYP4F11 MUTATED"       
clus
  CYP4F11 MUTATED CYP4F11 WILD-TYPE 
                1                78 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411        TCGA-KO-8413        TCGA-AK-3430 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4861 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ 
"CYP4F11 WILD-TYPE" "CYP4F11 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CYP4F11 MUTATED                    1                                 4
  CYP4F11 WILD-TYPE                 65                               437
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CYP4F11 MUTATED                                       0
  CYP4F11 WILD-TYPE                                   161
D29V9, multiclass
                                       clus
vv                                      CYP4F11 MUTATED CYP4F11 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   4               437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CYP4F11 MUTATED                                  0     0
  CYP4F11 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  CYP4F11 MUTATED                           0     5
  CYP4F11 WILD-TYPE                        65   564
D29V12, multiclass
                                  clus
vv                                 CYP4F11 MUTATED CYP4F11 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                65
  WHITE                                          5               564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                   cls
clus                  0   1
  CYP4F11 MUTATED     0   2
  CYP4F11 WILD-TYPE  32 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CYP4F11 MUTATED      0    2
  CYP4F11 WILD-TYPE   32  439
                        clus
vv                       CYP4F11 MUTATED CYP4F11 WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(30) Variable = STAG2 MUTATION ANALYSIS
D30V1, survival
                 sevent
clus2               0   1
  STAG2 MUTATED     9   4
  STAG2 WILD-TYPE 477 171
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             648 
  STAG2 MUTATED STAG2 WILD-TYPE 
              4             171 
$`STAG2 MUTATED`
TCGA-B0-4700 TCGA-B0-5709 TCGA-B0-5712 TCGA-BP-4985 TCGA-BP-5010 TCGA-CJ-4916 
       65.10       102.48        89.49        31.30        28.87        45.14 
TCGA-CZ-4859 TCGA-CZ-5466 TCGA-A4-7287 TCGA-A4-8098 TCGA-B3-4104 TCGA-BQ-5875 
       58.75        22.52        19.63        29.46        34.49        86.76 
TCGA-GL-A4EM 
        1.05 

$`STAG2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
        3.48        19.00         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36        92.98        47.97        96.36 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-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        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       69.21        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        47.54         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       18.21        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
        6.58        33.83        10.09        30.58        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5876 
        2.10        19.23         6.81         0.16        14.86        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68        27.65        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  STAG2 MUTATED STAG2 WILD-TYPE 
           1.05            0.07 
  STAG2 MUTATED STAG2 WILD-TYPE 
         102.48          194.79 
  STAG2 MUTATED STAG2 WILD-TYPE 
          34.49           34.24 
[1] "1.1 - 102.5 (34.5)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1"  
D30V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         4        1         7        2
  STAG2 WILD-TYPE     323       78       158       84
D30V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               4             323
  STAGE II              1              78
  STAGE III             7             158
  STAGE IV              2              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  STAG2 MUTATED     4   2   7   1
  STAG2 WILD-TYPE 336  95 214   9
D30V4, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  T1             4             336
  T2             2              95
  T3             7             214
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  STAG2 MUTATED     4   0   0
  STAG2 WILD-TYPE 268  36   6
D30V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             4             268
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                 cls
clus                0   1
  STAG2 MUTATED     9   2
  STAG2 WILD-TYPE 459  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      9    2
  STAG2 WILD-TYPE  459   76
   clus
vv  STAG2 MUTATED STAG2 WILD-TYPE
  0             9             459
  1             2              76
[1] 2 2
[1] FALSE
D30V7, binary
                 cls
clus                0   1
  STAG2 MUTATED     7   7
  STAG2 WILD-TYPE 222 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      7    7
  STAG2 WILD-TYPE  222  432
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             7             222
  MALE               7             432
[1] 2 2
[1] FALSE
D30V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  STAG2 MUTATED                    0                                 8
  STAG2 WILD-TYPE                 66                               433
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  STAG2 MUTATED                                       6
  STAG2 WILD-TYPE                                   155
D30V9, multiclass
                                       clus
vv                                      STAG2 MUTATED STAG2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 8             433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             6             155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAG2 MUTATED                                  0     0
  STAG2 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED                           2    10
  STAG2 WILD-TYPE                        63   559
D30V12, multiclass
                                  clus
vv                                 STAG2 MUTATED STAG2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    2              63
  WHITE                                       10             559
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                 cls
clus                0   1
  STAG2 MUTATED     0   9
  STAG2 WILD-TYPE  32 432
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      0    9
  STAG2 WILD-TYPE   32  432
                        clus
vv                       STAG2 MUTATED STAG2 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             9             432
[1] 2 2
[1] FALSE

Clustering(31) Variable = SKI MUTATION ANALYSIS
D31V1, survival
               sevent
clus2             0   1
  SKI MUTATED     7   2
  SKI WILD-TYPE 479 173
  SKI MUTATED SKI WILD-TYPE 
            9           652 
  SKI MUTATED SKI WILD-TYPE 
            2           173 
$`SKI MUTATED`
TCGA-KL-8330 TCGA-KO-8408 TCGA-AS-3777 TCGA-A4-7585 TCGA-B9-7268 TCGA-BQ-5884 
      108.62        16.67        40.70        35.18        22.06        26.04 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
       80.88        61.02        54.90 

$`SKI WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       37.58        38.40        31.27        28.04        12.13         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       51.19        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  SKI MUTATED SKI WILD-TYPE 
        16.67          0.07 
  SKI MUTATED SKI WILD-TYPE 
       108.62        194.79 
  SKI MUTATED SKI WILD-TYPE 
        40.70         34.09 
[1] "16.7 - 108.6 (40.7)" "0.1 - 194.8 (34.1)" 
[1] "hr=" "1.5"
D31V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  SKI MUTATED         5        2         2        0
  SKI WILD-TYPE     322       77       163       86
D31V3, multiclass
           clus
vv          SKI MUTATED SKI WILD-TYPE
  STAGE I             5           322
  STAGE II            2            77
  STAGE III           2           163
  STAGE IV            0            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
  SKI MUTATED     5   2   2   0
  SKI WILD-TYPE 335  95 219  10
D31V4, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  T1           5           335
  T2           2            95
  T3           2           219
  T4           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  SKI MUTATED     3   1   0
  SKI WILD-TYPE 269  35   6
D31V5, multiclass
    clus
vv   SKI MUTATED SKI WILD-TYPE
  N0           3           269
  N1           1            35
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
               cls
clus              0   1
  SKI MUTATED     5   0
  SKI WILD-TYPE 463  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      5    0
  SKI WILD-TYPE  463   78
   clus
vv  SKI MUTATED SKI WILD-TYPE
  0           5           463
  1           0            78
[1] 2 2
[1] FALSE
D31V7, binary
               cls
clus              0   1
  SKI MUTATED     2   7
  SKI WILD-TYPE 227 432
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      2    7
  SKI WILD-TYPE  227  432
        clus
vv       SKI MUTATED SKI WILD-TYPE
  FEMALE           2           227
  MALE             7           432
[1] 2 2
[1] FALSE
D31V8, continuous
               vv
clus            KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SKI MUTATED                    2                                 1
  SKI WILD-TYPE                 64                               440
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SKI MUTATED                                       6
  SKI WILD-TYPE                                   155
D31V9, multiclass
                                       clus
vv                                      SKI MUTATED SKI WILD-TYPE
  KIDNEY CHROMOPHOBE                              2            64
  KIDNEY CLEAR CELL RENAL CARCINOMA               1           440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           6           155
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
[1] "Remove cluster labels:" "SKI MUTATED"           
clus
  SKI MUTATED SKI WILD-TYPE 
            2            24 
   TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345    TCGA-KM-8639    TCGA-KN-8433 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-KO-8409    TCGA-B8-5158    TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-AL-3472    TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4117    TCGA-B9-A69E 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7963    TCGA-G7-7501    TCGA-GL-7773    TCGA-HE-A5NI 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
   TCGA-IA-A40U    TCGA-P4-A5E6    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" "SKI WILD-TYPE" 
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SKI MUTATED                                  0     0
  SKI WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  SKI MUTATED                           2     5
  SKI WILD-TYPE                        63   564
D31V12, multiclass
                                  clus
vv                                 SKI MUTATED SKI WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  2            63
  WHITE                                      5           564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
               cls
clus              0   1
  SKI MUTATED     0   5
  SKI WILD-TYPE  32 436
[1] "tbl2"
               cls
clus            [,1] [,2]
  SKI MUTATED      0    5
  SKI WILD-TYPE   32  436
                        clus
vv                       SKI MUTATED SKI WILD-TYPE
  HISPANIC OR LATINO               0            32
  NOT HISPANIC OR LATINO           5           436
[1] 2 2
[1] FALSE

Clustering(32) Variable = ARID1A MUTATION ANALYSIS
D32V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED    14   5
  ARID1A WILD-TYPE 472 170
  ARID1A MUTATED ARID1A WILD-TYPE 
              19              642 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5              170 
$`ARID1A MUTATED`
TCGA-B0-5102 TCGA-B0-5692 TCGA-B0-5713 TCGA-B8-5549 TCGA-BP-5199 TCGA-CJ-4892 
       90.87        48.89        61.32         6.38        44.55        50.01 
TCGA-CJ-4912 TCGA-CJ-6032 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-A4-8515 
       54.48        83.77        18.77        47.08        14.66        23.31 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-DW-7834 TCGA-G7-6796 TCGA-HE-A5NJ TCGA-J7-8537 
       63.72        43.20       129.86        34.82        56.75         0.13 
TCGA-PJ-A5Z8 
       12.85 

$`ARID1A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
       14.76       112.80       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        33.47        19.82        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       26.93        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-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        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        69.21        58.75        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 
       30.48        29.46        25.64        23.97        23.28        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       13.61        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        11.05        39.25        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       21.34        16.34        12.36        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       42.94         6.61        84.95        92.58        17.75        14.07 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.13             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
          129.86           194.79 
  ARID1A MUTATED ARID1A WILD-TYPE 
          47.080           33.665 
[1] "0.1 - 129.9 (47.1)" "0.1 - 194.8 (33.7)"
[1] "hr=" "1.2"
D32V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         7        4         6        1
  ARID1A WILD-TYPE     320       75       159       85
D32V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                7              320
  STAGE II               4               75
  STAGE III              6              159
  STAGE IV               1               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
  ARID1A MUTATED     8   4   7   0
  ARID1A WILD-TYPE 332  93 214  10
D32V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              8              332
  T2              4               93
  T3              7              214
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ARID1A MUTATED     6   3   0
  ARID1A WILD-TYPE 266  33   6
D32V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              6              266
  N1              3               33
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    15   1
  ARID1A WILD-TYPE 453  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     15    1
  ARID1A WILD-TYPE  453   77
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0             15              453
  1              1               77
[1] 2 2
[1] FALSE
D32V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     8  11
  ARID1A WILD-TYPE 221 428
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8   11
  ARID1A WILD-TYPE  221  428
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              8              221
  MALE               11              428
[1] 2 2
[1] FALSE
D32V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ARID1A MUTATED                    0                                11
  ARID1A WILD-TYPE                 66                               430
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ARID1A MUTATED                                       8
  ARID1A WILD-TYPE                                   153
D32V9, multiclass
                                       clus
vv                                      ARID1A MUTATED ARID1A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 11              430
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              8              153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               2               40 
      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-B8-4621 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A48D 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-B9-7268       TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NK       TCGA-IA-A40U       TCGA-IZ-A6M8 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9       TCGA-Q2-A5QZ 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
D32V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  1     1
  ARID1A WILD-TYPE                                1    10
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           0    16
  ARID1A WILD-TYPE                        65   553
D32V12, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         1               10
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                        16              553
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2  12
  ARID1A WILD-TYPE  30 429
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2   12
  ARID1A WILD-TYPE   30  429
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2               30
  NOT HISPANIC OR LATINO             12              429
[1] 2 2
[1] FALSE

Clustering(33) Variable = EGFR MUTATION ANALYSIS
D33V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     2   5
  EGFR WILD-TYPE 484 170
  EGFR MUTATED EGFR WILD-TYPE 
             7            654 
  EGFR MUTATED EGFR WILD-TYPE 
             5            170 
$`EGFR MUTATED`
TCGA-B0-4822 TCGA-B0-4849 TCGA-B0-5116 TCGA-B0-5713 TCGA-BP-4341 TCGA-BP-4354 
       36.53         2.27        21.60        61.32        52.24        33.99 
TCGA-CJ-4868 
       21.24 

$`EGFR WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77         6.02        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
        0.07        93.99        18.48        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        11.31        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 
       65.69        54.61        58.95        11.05        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  EGFR MUTATED EGFR WILD-TYPE 
          2.27           0.07 
  EGFR MUTATED EGFR WILD-TYPE 
         61.32         194.79 
  EGFR MUTATED EGFR WILD-TYPE 
        33.990         34.325 
[1] "2.3 - 61.3 (34.0)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "3.3"
D33V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EGFR MUTATED         0        1         4        2
  EGFR WILD-TYPE     327       78       161       84
D33V3, multiclass
           clus
vv          EGFR MUTATED EGFR WILD-TYPE
  STAGE I              0            327
  STAGE II             1             78
  STAGE III            4            161
  STAGE IV             2             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  EGFR MUTATED     0   1   5   1
  EGFR WILD-TYPE 340  96 216   9
D33V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            0            340
  T2            1             96
  T3            5            216
  T4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  EGFR MUTATED     3   1   0
  EGFR WILD-TYPE 269  35   6
D33V5, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  N0            3            269
  N1            1             35
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                cls
clus               0   1
  EGFR MUTATED     5   2
  EGFR WILD-TYPE 463  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      5    2
  EGFR WILD-TYPE  463   76
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            5            463
  1            2             76
[1] 2 2
[1] FALSE
D33V7, binary
                cls
clus               0   1
  EGFR MUTATED     1   6
  EGFR WILD-TYPE 228 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      1    6
  EGFR WILD-TYPE  228  433
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            1            228
  MALE              6            433
[1] 2 2
[1] FALSE
D33V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  EGFR MUTATED                    0                                 7
  EGFR WILD-TYPE                 66                               434
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  EGFR MUTATED                                       0
  EGFR WILD-TYPE                                   161
D33V9, multiclass
                                       clus
vv                                      EGFR MUTATED EGFR WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                7            434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            0            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EGFR MUTATED                                  0     0
  EGFR WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED                           0     7
  EGFR WILD-TYPE                        65   562
D33V12, multiclass
                                  clus
vv                                 EGFR MUTATED EGFR WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       7            562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                cls
clus               0   1
  EGFR MUTATED     0   5
  EGFR WILD-TYPE  32 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0    5
  EGFR WILD-TYPE   32  436
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            5            436
[1] 2 2
[1] FALSE

Clustering(34) Variable = DPCR1 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED     5   3
  DPCR1 WILD-TYPE 481 172
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              8             653 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              3             172 
$`DPCR1 MUTATED`
TCGA-KN-8435 TCGA-B0-5080 TCGA-CW-5589 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 
      115.00        11.24        78.18        61.41        47.01         1.94 
TCGA-DV-5576 TCGA-GL-A59R 
       23.90        12.43 

$`DPCR1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       60.59        63.39         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       11.67        66.28        56.84        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-HE-A5NF 
       12.92         3.68        27.65         1.05        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           1.94            0.07 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         115.00          194.79 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         35.455          34.290 
[1] "1.9 - 115.0 (35.5)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.3"
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DPCR1 MUTATED         3        1         1        3
  DPCR1 WILD-TYPE     324       78       164       83
D34V3, multiclass
           clus
vv          DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I               3             324
  STAGE II              1              78
  STAGE III             1             164
  STAGE IV              3              83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  DPCR1 MUTATED     3   1   4   0
  DPCR1 WILD-TYPE 337  96 217  10
D34V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             3             337
  T2             1              96
  T3             4             217
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  DPCR1 MUTATED     2   0   0
  DPCR1 WILD-TYPE 270  36   6
D34V5, multiclass
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              2             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5081 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-GL-7966      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
D34V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 465  75
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      3    3
  DPCR1 WILD-TYPE  465   75
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             3             465
  1             3              75
[1] 2 2
[1] FALSE
D34V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     2   6
  DPCR1 WILD-TYPE 227 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      2    6
  DPCR1 WILD-TYPE  227  433
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             2             227
  MALE               6             433
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5575      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  DPCR1 MUTATED                    1                                 6
  DPCR1 WILD-TYPE                 65                               435
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  DPCR1 MUTATED                                       1
  DPCR1 WILD-TYPE                                   160
D34V9, multiclass
                                       clus
vv                                      DPCR1 MUTATED DPCR1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DPCR1 MUTATED                                  0     0
  DPCR1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED                           1     7
  DPCR1 WILD-TYPE                        64   562
D34V12, multiclass
                                  clus
vv                                 DPCR1 MUTATED DPCR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        7             562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                 cls
clus                0   1
  DPCR1 MUTATED     0   8
  DPCR1 WILD-TYPE  32 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      0    8
  DPCR1 WILD-TYPE   32  433
                        clus
vv                       DPCR1 MUTATED DPCR1 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             8             433
[1] 2 2
[1] FALSE

Clustering(35) Variable = GUSB MUTATION ANALYSIS
D35V1, survival
                sevent
clus2              0   1
  GUSB MUTATED     2   2
  GUSB WILD-TYPE 484 173
  GUSB MUTATED GUSB WILD-TYPE 
             4            657 
  GUSB MUTATED GUSB WILD-TYPE 
             2            173 
$`GUSB MUTATED`
TCGA-B0-5095 TCGA-BP-4159 TCGA-CJ-4884 TCGA-CJ-4902 
        8.05        85.51        57.83        49.97 

$`GUSB WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09        10.95         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       14.30       111.02        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       39.45        59.44        50.24        56.35        47.67        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  GUSB MUTATED GUSB WILD-TYPE 
          8.05           0.07 
  GUSB MUTATED GUSB WILD-TYPE 
         85.51         194.79 
  GUSB MUTATED GUSB WILD-TYPE 
         53.90          34.19 
[1] "8.1 - 85.5 (53.9)"  "0.1 - 194.8 (34.2)"
[1] "hr=" "1.5"
D35V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GUSB MUTATED         1        0         3        0
  GUSB WILD-TYPE     326       79       162       86
D35V3, multiclass
           clus
vv          GUSB MUTATED GUSB WILD-TYPE
  STAGE I              1            326
  STAGE II             0             79
  STAGE III            3            162
  STAGE IV             0             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
  GUSB MUTATED     1   0   3   0
  GUSB WILD-TYPE 339  97 218  10
D35V4, multiclass
    clus
vv   GUSB MUTATED GUSB WILD-TYPE
  T1            1            339
  T2            0             97
  T3            3            218
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GUSB MUTATED     2   0   0
  GUSB WILD-TYPE 270  36   6
D35V5, multiclass
[1] "Remove cluster labels:" "GUSB MUTATED"          
clus
  GUSB MUTATED GUSB WILD-TYPE 
             2            312 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3380     TCGA-A3-3385 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3425     TCGA-AK-3427     TCGA-AK-3428 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AK-3450     TCGA-AK-3451     TCGA-AK-3456     TCGA-B0-4690 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4691     TCGA-B0-4693     TCGA-B0-4703     TCGA-B0-4710 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4814     TCGA-B0-4816 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4817     TCGA-B0-4823     TCGA-B0-4824     TCGA-B0-4827 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4833     TCGA-B0-4837     TCGA-B0-4838     TCGA-B0-4839 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4842     TCGA-B0-4843     TCGA-B0-4846     TCGA-B0-4852 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-4945     TCGA-B0-5075     TCGA-B0-5077     TCGA-B0-5080 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5081     TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5096 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5697     TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4158     TCGA-BP-4160     TCGA-BP-4162 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331     TCGA-BP-4337 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342     TCGA-BP-4343 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4795 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799     TCGA-BP-4960 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4986 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995     TCGA-BP-5006 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198     TCGA-BP-5199 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638     TCGA-CJ-4639 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891     TCGA-CJ-4892 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904     TCGA-CJ-4918 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033     TCGA-CW-5585 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4856 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" "GUSB WILD-TYPE" 
D35V6, binary
                cls
clus               0   1
  GUSB MUTATED     4   0
  GUSB WILD-TYPE 464  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      4    0
  GUSB WILD-TYPE  464   78
   clus
vv  GUSB MUTATED GUSB WILD-TYPE
  0            4            464
  1            0             78
[1] 2 2
[1] FALSE
D35V7, binary
                cls
clus               0   1
  GUSB MUTATED     1   3
  GUSB WILD-TYPE 228 436
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      1    3
  GUSB WILD-TYPE  228  436
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  FEMALE            1            228
  MALE              3            436
[1] 2 2
[1] FALSE
D35V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GUSB MUTATED                    0                                 4
  GUSB WILD-TYPE                 66                               437
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GUSB MUTATED                                       0
  GUSB WILD-TYPE                                   161
D35V9, multiclass
                                       clus
vv                                      GUSB MUTATED GUSB WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                4            437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            0            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
D35V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GUSB MUTATED                                  0     0
  GUSB WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GUSB MUTATED                           0     4
  GUSB WILD-TYPE                        65   565
D35V12, multiclass
                                  clus
vv                                 GUSB MUTATED GUSB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       4            565
[1] 4 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
  GUSB MUTATED     0   3
  GUSB WILD-TYPE  32 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      0    3
  GUSB WILD-TYPE   32  438
                        clus
vv                       GUSB MUTATED GUSB WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(36) Variable = MED16 MUTATION ANALYSIS
D36V1, survival
                 sevent
clus2               0   1
  MED16 MUTATED     2   1
  MED16 WILD-TYPE 484 174
  MED16 MUTATED MED16 WILD-TYPE 
              3             658 
  MED16 MUTATED MED16 WILD-TYPE 
              1             174 
$`MED16 MUTATED`
TCGA-CZ-5986 TCGA-BQ-5890 TCGA-G7-6789 
       12.26         7.66         4.01 

$`MED16 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       31.10        12.69        80.19        67.96        65.65        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  MED16 MUTATED MED16 WILD-TYPE 
           4.01            0.07 
  MED16 MUTATED MED16 WILD-TYPE 
          12.26          194.79 
  MED16 MUTATED MED16 WILD-TYPE 
          7.660          34.375 
[1] "4.0 - 12.3 (7.7)"   "0.1 - 194.8 (34.4)"
[1] "hr=" "6.4"
D36V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  MED16 MUTATED         1        0         2        1
  MED16 WILD-TYPE     326       79       163       85
D36V3, multiclass
           clus
vv          MED16 MUTATED MED16 WILD-TYPE
  STAGE I               1             326
  STAGE II              0              79
  STAGE III             2             163
  STAGE IV              1              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
  MED16 MUTATED     1   0   3   0
  MED16 WILD-TYPE 339  97 218  10
D36V4, multiclass
    clus
vv   MED16 MUTATED MED16 WILD-TYPE
  T1             1             339
  T2             0              97
  T3             3             218
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  MED16 MUTATED     2   0   1
  MED16 WILD-TYPE 270  36   5
D36V5, multiclass
    clus
vv   MED16 MUTATED MED16 WILD-TYPE
  N0             2             270
  N1             0              36
  N2             1               5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                 cls
clus                0   1
  MED16 MUTATED     3   0
  MED16 WILD-TYPE 465  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      3    0
  MED16 WILD-TYPE  465   78
   clus
vv  MED16 MUTATED MED16 WILD-TYPE
  0             3             465
  1             0              78
[1] 2 2
[1] FALSE
D36V7, binary
                 cls
clus                0   1
  MED16 MUTATED     2   2
  MED16 WILD-TYPE 227 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      2    2
  MED16 WILD-TYPE  227  437
        clus
vv       MED16 MUTATED MED16 WILD-TYPE
  FEMALE             2             227
  MALE               2             437
[1] 2 2
[1] FALSE
D36V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  MED16 MUTATED                    0                                 1
  MED16 WILD-TYPE                 66                               440
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  MED16 MUTATED                                       3
  MED16 WILD-TYPE                                   158
D36V9, multiclass
                                       clus
vv                                      MED16 MUTATED MED16 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 1             440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  MED16 MUTATED                                  0     0
  MED16 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  MED16 MUTATED                           0     3
  MED16 WILD-TYPE                        65   566
D36V12, multiclass
                                  clus
vv                                 MED16 MUTATED MED16 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              65
  WHITE                                        3             566
[1] 4 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
  MED16 MUTATED     0   2
  MED16 WILD-TYPE  32 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED16 MUTATED      0    2
  MED16 WILD-TYPE   32  439
                        clus
vv                       MED16 MUTATED MED16 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             2             439
[1] 2 2
[1] FALSE

Clustering(37) Variable = PTCH1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED     5   3
  PTCH1 WILD-TYPE 481 172
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              8             653 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              3             172 
$`PTCH1 MUTATED`
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4814 TCGA-B8-4153 TCGA-BP-4337 TCGA-BP-4768 
        6.64        20.25         5.52        25.05         0.07        13.15 
TCGA-BP-4777 TCGA-A4-7732 
       56.91        19.13 

$`PTCH1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        3.16        43.96         3.25        15.72        46.59         0.59 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4619 
       23.31        16.80        27.16        27.55        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4771 
       44.15        41.75        71.80        48.07        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       61.97        60.59        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.07            0.10 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          56.91          194.79 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          16.14           34.49 
[1] "0.1 - 56.9 (16.1)"  "0.1 - 194.8 (34.5)"
[1] "hr=" "3"  
D37V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTCH1 MUTATED         2        0         4        1
  PTCH1 WILD-TYPE     325       79       161       85
D37V3, multiclass
           clus
vv          PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I               2             325
  STAGE II              0              79
  STAGE III             4             161
  STAGE IV              1              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
  PTCH1 MUTATED     2   1   4   1
  PTCH1 WILD-TYPE 338  96 217   9
D37V4, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             2             338
  T2             1              96
  T3             4             217
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  PTCH1 MUTATED     3   0   0
  PTCH1 WILD-TYPE 269  36   6
D37V5, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  N0             3             269
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED     6   1
  PTCH1 WILD-TYPE 462  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      6    1
  PTCH1 WILD-TYPE  462   77
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0             6             462
  1             1              77
[1] 2 2
[1] FALSE
D37V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED     3   5
  PTCH1 WILD-TYPE 226 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    5
  PTCH1 WILD-TYPE  226  434
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE             3             226
  MALE               5             434
[1] 2 2
[1] FALSE
D37V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PTCH1 MUTATED                    0                                 7
  PTCH1 WILD-TYPE                 66                               434
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PTCH1 MUTATED                                       1
  PTCH1 WILD-TYPE                                   160
D37V9, multiclass
                                       clus
vv                                      PTCH1 MUTATED PTCH1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 7             434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTCH1 MUTATED                                  0     0
  PTCH1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED                           1     7
  PTCH1 WILD-TYPE                        64   562
D37V12, multiclass
                                  clus
vv                                 PTCH1 MUTATED PTCH1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        7             562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                 cls
clus                0   1
  PTCH1 MUTATED     0   6
  PTCH1 WILD-TYPE  32 435
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      0    6
  PTCH1 WILD-TYPE   32  435
                        clus
vv                       PTCH1 MUTATED PTCH1 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             6             435
[1] 2 2
[1] FALSE

Clustering(38) Variable = AHNAK2 MUTATION ANALYSIS
D38V1, survival
                  sevent
clus2                0   1
  AHNAK2 MUTATED    23  10
  AHNAK2 WILD-TYPE 463 165
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              33              628 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
              10              165 
$`AHNAK2 MUTATED`
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8337 TCGA-KL-8341 TCGA-KN-8419 TCGA-KN-8423 
       90.48       108.62        44.84        24.79        23.47        25.91 
TCGA-KN-8428 TCGA-KO-8404 TCGA-KO-8413 TCGA-KO-8414 TCGA-AK-3425 TCGA-AK-3454 
       52.27        10.68        86.10        77.85       109.91        28.73 
TCGA-AK-3456 TCGA-B0-4710 TCGA-B0-4847 TCGA-B0-5098 TCGA-B0-5099 TCGA-B4-5843 
       37.58         3.16        26.07        52.08        15.95         0.36 
TCGA-BP-4162 TCGA-BP-4341 TCGA-BP-4981 TCGA-BP-4995 TCGA-BP-5200 TCGA-CJ-4643 
      101.06        52.24        36.07        45.07        34.95        58.95 
TCGA-CJ-4644 TCGA-CW-5583 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5882 TCGA-BQ-7060 
       11.05        81.83        19.56         0.46        21.63         7.04 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-GL-7773 
       54.90        34.19        12.92 

$`AHNAK2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       87.91        25.48        65.19       104.52         3.55         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38        87.78       103.27        57.17        61.58 
TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 
       63.95        39.16        49.08        49.02        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 
       37.38        48.82        52.93        45.53        88.37        42.97 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       43.20        55.76        18.64        28.31        65.52        20.28 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       67.20        57.37        46.78        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       45.93        22.45        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 
       19.00        65.10         5.98         2.14        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4849 
       11.64        10.29        65.29        39.45        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        8.05         2.24        21.86        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         5.46         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        43.00        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
       13.41        24.62        33.47        19.82        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       75.88        65.69        54.61        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 
       83.77         7.36        64.57        92.02        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       44.61         2.20        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 
       12.46        50.50        28.18        26.40        20.61        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       50.40        49.84        26.27        11.28         7.63         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       80.88        51.19        61.02        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 
       25.15        13.68        25.84         6.38       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
            0.36             0.07 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
          109.91           194.79 
  AHNAK2 MUTATED AHNAK2 WILD-TYPE 
           34.95            34.14 
[1] "0.4 - 109.9 (35.0)" "0.1 - 194.8 (34.1)"
[1] "hr=" "1.1"
D38V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  AHNAK2 MUTATED        14        8         6        4
  AHNAK2 WILD-TYPE     313       71       159       82
D38V3, multiclass
           clus
vv          AHNAK2 MUTATED AHNAK2 WILD-TYPE
  STAGE I               14              313
  STAGE II               8               71
  STAGE III              6              159
  STAGE IV               4               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                T1  T2  T3  T4
  AHNAK2 MUTATED    14   9   9   1
  AHNAK2 WILD-TYPE 326  88 212   9
D38V4, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  T1             14              326
  T2              9               88
  T3              9              212
  T4              1                9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  AHNAK2 MUTATED    18   0   1
  AHNAK2 WILD-TYPE 254  36   5
D38V5, multiclass
    clus
vv   AHNAK2 MUTATED AHNAK2 WILD-TYPE
  N0             18              254
  N1              0               36
  N2              1                5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED    24   2
  AHNAK2 WILD-TYPE 444  76
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED     24    2
  AHNAK2 WILD-TYPE  444   76
   clus
vv  AHNAK2 MUTATED AHNAK2 WILD-TYPE
  0             24              444
  1              2               76
[1] 2 2
[1] FALSE
D38V7, binary
                  cls
clus                 0   1
  AHNAK2 MUTATED    13  20
  AHNAK2 WILD-TYPE 216 419
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED     13   20
  AHNAK2 WILD-TYPE  216  419
        clus
vv       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  FEMALE             13              216
  MALE               20              419
[1] 2 2
[1] FALSE
D38V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  AHNAK2 MUTATED                   10                                16
  AHNAK2 WILD-TYPE                 56                               425
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  AHNAK2 MUTATED                                       7
  AHNAK2 WILD-TYPE                                   154
D38V9, multiclass
                                       clus
vv                                      AHNAK2 MUTATED AHNAK2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                10               56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 16              425
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              7              154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AHNAK2 MUTATED                                  1     2
  AHNAK2 WILD-TYPE                                1     9
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  AHNAK2 MUTATED                           6    22
  AHNAK2 WILD-TYPE                        59   547
D38V12, multiclass
                                  clus
vv                                 AHNAK2 MUTATED AHNAK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                1
  ASIAN                                         2                9
  BLACK OR AFRICAN AMERICAN                     6               59
  WHITE                                        22              547
[1] 4 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
  AHNAK2 MUTATED     2  20
  AHNAK2 WILD-TYPE  30 421
[1] "tbl2"
                  cls
clus               [,1] [,2]
  AHNAK2 MUTATED      2   20
  AHNAK2 WILD-TYPE   30  421
                        clus
vv                       AHNAK2 MUTATED AHNAK2 WILD-TYPE
  HISPANIC OR LATINO                  2               30
  NOT HISPANIC OR LATINO             20              421
[1] 2 2
[1] FALSE

Clustering(39) Variable = RLIM MUTATION ANALYSIS
D39V1, survival
                sevent
clus2              0   1
  RLIM MUTATED     7   2
  RLIM WILD-TYPE 479 173
  RLIM MUTATED RLIM WILD-TYPE 
             9            652 
  RLIM MUTATED RLIM WILD-TYPE 
             2            173 
$`RLIM MUTATED`
TCGA-KN-8426 TCGA-AK-3453 TCGA-AK-3454 TCGA-B0-4817 TCGA-CZ-4865 TCGA-A4-7996 
        3.55        45.93        28.73        33.50         5.46        16.64 
TCGA-AL-3473 TCGA-BQ-5876 TCGA-BQ-5885 
       25.08        19.27        30.28 

$`RLIM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         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        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3455 TCGA-AK-3456 
       46.78        42.08        58.49        48.69        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       52.21        45.07        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        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       92.98       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7997 
        0.10        35.18        19.13         0.89         0.23        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       30.35        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
        6.81         0.16        14.86        86.76         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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  RLIM MUTATED RLIM WILD-TYPE 
          3.55           0.07 
  RLIM MUTATED RLIM WILD-TYPE 
         45.93         194.79 
  RLIM MUTATED RLIM WILD-TYPE 
        25.080         34.655 
[1] "3.5 - 45.9 (25.1)"  "0.1 - 194.8 (34.7)"
[1] "hr=" "1.5"
D39V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RLIM MUTATED         4        2         2        1
  RLIM WILD-TYPE     323       77       163       85
D39V3, multiclass
           clus
vv          RLIM MUTATED RLIM WILD-TYPE
  STAGE I              4            323
  STAGE II             2             77
  STAGE III            2            163
  STAGE IV             1             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
  RLIM MUTATED     4   2   3   0
  RLIM WILD-TYPE 336  95 218  10
D39V4, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  T1            4            336
  T2            2             95
  T3            3            218
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RLIM MUTATED     3   0   0
  RLIM WILD-TYPE 269  36   6
D39V5, multiclass
    clus
vv   RLIM MUTATED RLIM WILD-TYPE
  N0            3            269
  N1            0             36
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                cls
clus               0   1
  RLIM MUTATED     7   1
  RLIM WILD-TYPE 461  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      7    1
  RLIM WILD-TYPE  461   77
   clus
vv  RLIM MUTATED RLIM WILD-TYPE
  0            7            461
  1            1             77
[1] 2 2
[1] FALSE
D39V7, binary
                cls
clus               0   1
  RLIM MUTATED     3   6
  RLIM WILD-TYPE 226 433
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      3    6
  RLIM WILD-TYPE  226  433
        clus
vv       RLIM MUTATED RLIM WILD-TYPE
  FEMALE            3            226
  MALE              6            433
[1] 2 2
[1] FALSE
D39V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RLIM MUTATED                    1                                 4
  RLIM WILD-TYPE                 65                               437
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RLIM MUTATED                                       4
  RLIM WILD-TYPE                                   157
D39V9, multiclass
                                       clus
vv                                      RLIM MUTATED RLIM WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                4            437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            4            157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RLIM MUTATED                                  0     0
  RLIM WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RLIM MUTATED                           0     9
  RLIM WILD-TYPE                        65   560
D39V12, multiclass
                                  clus
vv                                 RLIM MUTATED RLIM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       9            560
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                cls
clus               0   1
  RLIM MUTATED     0   7
  RLIM WILD-TYPE  32 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  RLIM MUTATED      0    7
  RLIM WILD-TYPE   32  434
                        clus
vv                       RLIM MUTATED RLIM WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            7            434
[1] 2 2
[1] FALSE

Clustering(40) Variable = SLC23A1 MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  SLC23A1 MUTATED     6   1
  SLC23A1 WILD-TYPE 480 174
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                7               654 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
                1               174 
$`SLC23A1 MUTATED`
TCGA-A3-3322 TCGA-A3-3370 TCGA-B0-4714 TCGA-B0-5712 TCGA-CJ-4634 TCGA-BQ-5878 
       48.59        74.76         3.25        89.49        59.84        63.72 
TCGA-MH-A55Z 
       27.78 

$`SLC23A1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.08        49.02        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.63        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        6.64        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       79.36        92.98       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
             3.25              0.07 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
            89.49            194.79 
  SLC23A1 MUTATED SLC23A1 WILD-TYPE 
            59.84             34.09 
[1] "3.2 - 89.5 (59.8)"  "0.1 - 194.8 (34.1)"
[1] "hr=" "2.5"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC23A1 MUTATED         4        0         1        2
  SLC23A1 WILD-TYPE     323       79       164       84
D40V3, multiclass
           clus
vv          SLC23A1 MUTATED SLC23A1 WILD-TYPE
  STAGE I                 4               323
  STAGE II                0                79
  STAGE III               1               164
  STAGE IV                2                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  SLC23A1 MUTATED     4   1   2   0
  SLC23A1 WILD-TYPE 336  96 219  10
D40V4, multiclass
    clus
vv   SLC23A1 MUTATED SLC23A1 WILD-TYPE
  T1               4               336
  T2               1                96
  T3               2               219
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC23A1 MUTATED     2   1   0
  SLC23A1 WILD-TYPE 270  35   6
D40V5, multiclass
    clus
vv   SLC23A1 MUTATED SLC23A1 WILD-TYPE
  N0               2               270
  N1               1                35
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  SLC23A1 MUTATED     4   2
  SLC23A1 WILD-TYPE 464  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      4    2
  SLC23A1 WILD-TYPE  464   76
   clus
vv  SLC23A1 MUTATED SLC23A1 WILD-TYPE
  0               4               464
  1               2                76
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  SLC23A1 MUTATED     4   3
  SLC23A1 WILD-TYPE 225 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      4    3
  SLC23A1 WILD-TYPE  225  436
        clus
vv       SLC23A1 MUTATED SLC23A1 WILD-TYPE
  FEMALE               4               225
  MALE                 3               436
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC23A1 MUTATED                    0                                 5
  SLC23A1 WILD-TYPE                 66                               436
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC23A1 MUTATED                                       2
  SLC23A1 WILD-TYPE                                   159
D40V9, multiclass
                                       clus
vv                                      SLC23A1 MUTATED SLC23A1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   5               436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC23A1 MUTATED                                  0     0
  SLC23A1 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC23A1 MUTATED                           2     5
  SLC23A1 WILD-TYPE                        63   564
D40V12, multiclass
                                  clus
vv                                 SLC23A1 MUTATED SLC23A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      2                63
  WHITE                                          5               564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                   cls
clus                  0   1
  SLC23A1 MUTATED     0   5
  SLC23A1 WILD-TYPE  32 436
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC23A1 MUTATED      0    5
  SLC23A1 WILD-TYPE   32  436
                        clus
vv                       SLC23A1 MUTATED SLC23A1 WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               5               436
[1] 2 2
[1] FALSE

Clustering(41) Variable = STAM MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  STAM MUTATED     4   2
  STAM WILD-TYPE 482 173
  STAM MUTATED STAM WILD-TYPE 
             6            655 
  STAM MUTATED STAM WILD-TYPE 
             2            173 
$`STAM MUTATED`
TCGA-KN-8435 TCGA-KO-8404 TCGA-BP-5200 TCGA-CJ-4639 TCGA-BQ-5889 TCGA-BQ-5894 
      115.00        10.68        34.95        75.88        10.88         2.76 

$`STAM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       44.55        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22        14.17        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25         7.66         0.95        11.97         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  STAM MUTATED STAM WILD-TYPE 
          2.76           0.07 
  STAM MUTATED STAM WILD-TYPE 
        115.00         194.79 
  STAM MUTATED STAM WILD-TYPE 
        22.915         34.290 
[1] "2.8 - 115.0 (22.9)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.3"
D41V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  STAM MUTATED         0        3         0        3
  STAM WILD-TYPE     327       76       165       83
D41V3, multiclass
           clus
vv          STAM MUTATED STAM WILD-TYPE
  STAGE I              0            327
  STAGE II             3             76
  STAGE III            0            165
  STAGE IV             3             83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  STAM MUTATED     0   3   2   1
  STAM WILD-TYPE 340  94 219   9
D41V4, multiclass
    clus
vv   STAM MUTATED STAM WILD-TYPE
  T1            0            340
  T2            3             94
  T3            2            219
  T4            1              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  STAM MUTATED     1   2   0
  STAM WILD-TYPE 271  34   6
D41V5, multiclass
    clus
vv   STAM MUTATED STAM WILD-TYPE
  N0            1            271
  N1            2             34
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                cls
clus               0   1
  STAM MUTATED     2   2
  STAM WILD-TYPE 466  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      2    2
  STAM WILD-TYPE  466   76
   clus
vv  STAM MUTATED STAM WILD-TYPE
  0            2            466
  1            2             76
[1] 2 2
[1] FALSE
D41V7, binary
                cls
clus               0   1
  STAM MUTATED     1   5
  STAM WILD-TYPE 228 434
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      1    5
  STAM WILD-TYPE  228  434
        clus
vv       STAM MUTATED STAM WILD-TYPE
  FEMALE            1            228
  MALE              5            434
[1] 2 2
[1] FALSE
D41V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  STAM MUTATED                    2                                 2
  STAM WILD-TYPE                 64                               439
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  STAM MUTATED                                       2
  STAM WILD-TYPE                                   159
D41V9, multiclass
                                       clus
vv                                      STAM MUTATED STAM WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                2            439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  STAM MUTATED                                  0     0
  STAM WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  STAM MUTATED                           0     5
  STAM WILD-TYPE                        65   564
D41V12, multiclass
                                  clus
vv                                 STAM MUTATED STAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       5            564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                cls
clus               0   1
  STAM MUTATED     2   3
  STAM WILD-TYPE  30 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  STAM MUTATED      2    3
  STAM WILD-TYPE   30  438
                        clus
vv                       STAM MUTATED STAM WILD-TYPE
  HISPANIC OR LATINO                2             30
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(42) Variable = RHEB MUTATION ANALYSIS
D42V1, survival
                sevent
clus2              0   1
  RHEB MUTATED     3   1
  RHEB WILD-TYPE 483 174
  RHEB MUTATED RHEB WILD-TYPE 
             4            657 
  RHEB MUTATED RHEB WILD-TYPE 
             1            174 
$`RHEB MUTATED`
TCGA-AK-3450 TCGA-CJ-4895 TCGA-CJ-5686 TCGA-Q2-A5QZ 
       58.49        39.45        67.00        14.07 

$`RHEB WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       57.37        46.78        42.08        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        27.65        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       92.58        12.85        17.75 

  RHEB MUTATED RHEB WILD-TYPE 
         14.07           0.07 
  RHEB MUTATED RHEB WILD-TYPE 
         67.00         194.79 
  RHEB MUTATED RHEB WILD-TYPE 
         48.97          34.19 
[1] "14.1 - 67.0 (49.0)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.2"
D42V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHEB MUTATED         2        0         1        1
  RHEB WILD-TYPE     325       79       164       85
D42V3, multiclass
           clus
vv          RHEB MUTATED RHEB WILD-TYPE
  STAGE I              2            325
  STAGE II             0             79
  STAGE III            1            164
  STAGE IV             1             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
  RHEB MUTATED     2   0   2   0
  RHEB WILD-TYPE 338  97 219  10
D42V4, multiclass
    clus
vv   RHEB MUTATED RHEB WILD-TYPE
  T1            2            338
  T2            0             97
  T3            2            219
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RHEB MUTATED     1   0   0
  RHEB WILD-TYPE 271  36   6
D42V5, multiclass
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1            313 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3380     TCGA-A3-3385 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3425     TCGA-AK-3427     TCGA-AK-3428 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AK-3451     TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4693     TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4823     TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4837     TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4843     TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5075     TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5697     TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5641     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-B8-4148 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5553     TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4169     TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4326     TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4795     TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4960     TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-4986     TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-5182     TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BP-5199     TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CJ-4892     TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CJ-4918     TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B1-A657     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-BQ-7058     TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-P4-A5EA 
"RHEB WILD-TYPE" 
D42V6, binary
                cls
clus               0   1
  RHEB MUTATED     2   1
  RHEB WILD-TYPE 466  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      2    1
  RHEB WILD-TYPE  466   77
   clus
vv  RHEB MUTATED RHEB WILD-TYPE
  0            2            466
  1            1             77
[1] 2 2
[1] FALSE
D42V7, binary
                cls
clus               0   1
  RHEB MUTATED     3   1
  RHEB WILD-TYPE 226 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      3    1
  RHEB WILD-TYPE  226  438
        clus
vv       RHEB MUTATED RHEB WILD-TYPE
  FEMALE            3            226
  MALE              1            438
[1] 2 2
[1] FALSE
D42V8, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             78 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411     TCGA-KO-8413     TCGA-AK-3430 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     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-EU-5904     TCGA-EU-5905 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7834     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-DW-7963 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-G7-7502     TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40Y     TCGA-J7-8537 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RHEB MUTATED                    0                                 3
  RHEB WILD-TYPE                 66                               438
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RHEB MUTATED                                       1
  RHEB WILD-TYPE                                   160
D42V9, multiclass
                                       clus
vv                                      RHEB MUTATED RHEB WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                3            438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             41 
    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-B8-4621 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B8-5158     TCGA-B8-5164     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-B9-4115     TCGA-B9-4117 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-A59T     TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-IA-A40U     TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-PJ-A5Z9 
"RHEB WILD-TYPE" 
D42V11, continuous
[1] "Remove cluster labels:" "RHEB MUTATED"          
clus
  RHEB MUTATED RHEB WILD-TYPE 
             1             25 
    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-B8-5158     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-GL-7773     TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6 
"RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" "RHEB WILD-TYPE" 
    TCGA-PJ-A5Z9 
"RHEB WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RHEB MUTATED                                  0     0
  RHEB WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RHEB MUTATED                           1     3
  RHEB WILD-TYPE                        64   566
D42V12, multiclass
                                  clus
vv                                 RHEB MUTATED RHEB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             64
  WHITE                                       3            566
[1] 4 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
  RHEB MUTATED     0   4
  RHEB WILD-TYPE  32 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHEB MUTATED      0    4
  RHEB WILD-TYPE   32  437
                        clus
vv                       RHEB MUTATED RHEB WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            4            437
[1] 2 2
[1] FALSE

Clustering(43) Variable = SLC4A8 MUTATION ANALYSIS
D43V1, survival
                  sevent
clus2                0   1
  SLC4A8 MUTATED     5   1
  SLC4A8 WILD-TYPE 481 174
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               6              655 
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               1              174 
$`SLC4A8 MUTATED`
TCGA-KN-8424 TCGA-KO-8411 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-4694 TCGA-CZ-5466 
       65.19       103.27        68.61        42.08         3.48        22.52 

$`SLC4A8 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67        80.38        87.78        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3450 
       15.78        60.92        67.20        57.37        46.78        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        4.57         2.53        19.00        65.10         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 
       20.94        43.30        11.24        11.90        34.36         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       32.61        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       10.36        21.57         9.57         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.53        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        47.54         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
            3.48             0.07 
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
          103.27           194.79 
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
          53.635           34.190 
[1] "3.5 - 103.3 (53.6)" "0.1 - 194.8 (34.2)"
[1] "hr=" "2"  
D43V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SLC4A8 MUTATED         3        0         3        0
  SLC4A8 WILD-TYPE     324       79       162       86
D43V3, multiclass
           clus
vv          SLC4A8 MUTATED SLC4A8 WILD-TYPE
  STAGE I                3              324
  STAGE II               0               79
  STAGE III              3              162
  STAGE IV               0               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
  SLC4A8 MUTATED     3   0   3   0
  SLC4A8 WILD-TYPE 337  97 218  10
D43V4, multiclass
    clus
vv   SLC4A8 MUTATED SLC4A8 WILD-TYPE
  T1              3              337
  T2              0               97
  T3              3              218
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SLC4A8 MUTATED     1   0   0
  SLC4A8 WILD-TYPE 271  36   6
D43V5, multiclass
[1] "Remove cluster labels:" "SLC4A8 MUTATED"        
clus
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               1              313 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362       TCGA-A3-3363 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373       TCGA-A3-3374 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385       TCGA-A3-3387 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B1-A657       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BQ-5891       TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BQ-7045       TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-BQ-7058       TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-J7-6720       TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-P4-A5EA 
"SLC4A8 WILD-TYPE" 
D43V6, binary
                  cls
clus                 0   1
  SLC4A8 MUTATED     5   0
  SLC4A8 WILD-TYPE 463  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A8 MUTATED      5    0
  SLC4A8 WILD-TYPE  463   78
   clus
vv  SLC4A8 MUTATED SLC4A8 WILD-TYPE
  0              5              463
  1              0               78
[1] 2 2
[1] FALSE
D43V7, binary
                  cls
clus                 0   1
  SLC4A8 MUTATED     1   5
  SLC4A8 WILD-TYPE 228 434
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A8 MUTATED      1    5
  SLC4A8 WILD-TYPE  228  434
        clus
vv       SLC4A8 MUTATED SLC4A8 WILD-TYPE
  FEMALE              1              228
  MALE                5              434
[1] 2 2
[1] FALSE
D43V8, continuous
[1] "Remove cluster labels:" "SLC4A8 MUTATED"        
clus
  SLC4A8 MUTATED SLC4A8 WILD-TYPE 
               1               78 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8413       TCGA-AK-3430       TCGA-B0-4838 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5465 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ 
"SLC4A8 WILD-TYPE" "SLC4A8 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC4A8 MUTATED                    2                                 4
  SLC4A8 WILD-TYPE                 64                               437
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC4A8 MUTATED                                       0
  SLC4A8 WILD-TYPE                                   161
D43V9, multiclass
                                       clus
vv                                      SLC4A8 MUTATED SLC4A8 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 2               64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              0              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC4A8 MUTATED                                  0     0
  SLC4A8 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SLC4A8 MUTATED                           0     5
  SLC4A8 WILD-TYPE                        65   564
D43V12, multiclass
                                  clus
vv                                 SLC4A8 MUTATED SLC4A8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         5              564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                  cls
clus                 0   1
  SLC4A8 MUTATED     0   4
  SLC4A8 WILD-TYPE  32 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SLC4A8 MUTATED      0    4
  SLC4A8 WILD-TYPE   32  437
                        clus
vv                       SLC4A8 MUTATED SLC4A8 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              4              437
[1] 2 2
[1] FALSE

Clustering(44) Variable = RUFY3 MUTATION ANALYSIS
D44V1, survival
                 sevent
clus2               0   1
  RUFY3 MUTATED     6   1
  RUFY3 WILD-TYPE 480 174
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              7             654 
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              1             174 
$`RUFY3 MUTATED`
TCGA-KL-8330 TCGA-B0-5094 TCGA-B2-4099 TCGA-BP-4994 TCGA-B3-3925 TCGA-GL-A59R 
      108.62        10.95        12.30        43.00        33.83        12.43 
TCGA-MH-A561 
       27.65 

$`RUFY3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        6.58        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.78        30.38        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  RUFY3 MUTATED RUFY3 WILD-TYPE 
          10.95            0.07 
  RUFY3 MUTATED RUFY3 WILD-TYPE 
         108.62          194.79 
  RUFY3 MUTATED RUFY3 WILD-TYPE 
         27.650          34.375 
[1] "10.9 - 108.6 (27.6)" "0.1 - 194.8 (34.4)" 
[1] "hr=" "1.6"
D44V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RUFY3 MUTATED         3        1         2        1
  RUFY3 WILD-TYPE     324       78       163       85
D44V3, multiclass
           clus
vv          RUFY3 MUTATED RUFY3 WILD-TYPE
  STAGE I               3             324
  STAGE II              1              78
  STAGE III             2             163
  STAGE IV              1              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
  RUFY3 MUTATED     3   1   3   0
  RUFY3 WILD-TYPE 337  96 218  10
D44V4, multiclass
    clus
vv   RUFY3 MUTATED RUFY3 WILD-TYPE
  T1             3             337
  T2             1              96
  T3             3             218
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RUFY3 MUTATED     3   0   0
  RUFY3 WILD-TYPE 269  36   6
D44V5, multiclass
    clus
vv   RUFY3 MUTATED RUFY3 WILD-TYPE
  N0             3             269
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                 cls
clus                0   1
  RUFY3 MUTATED     4   1
  RUFY3 WILD-TYPE 464  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY3 MUTATED      4    1
  RUFY3 WILD-TYPE  464   77
   clus
vv  RUFY3 MUTATED RUFY3 WILD-TYPE
  0             4             464
  1             1              77
[1] 2 2
[1] FALSE
D44V7, binary
                 cls
clus                0   1
  RUFY3 MUTATED     1   6
  RUFY3 WILD-TYPE 228 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY3 MUTATED      1    6
  RUFY3 WILD-TYPE  228  433
        clus
vv       RUFY3 MUTATED RUFY3 WILD-TYPE
  FEMALE             1             228
  MALE               6             433
[1] 2 2
[1] FALSE
D44V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RUFY3 MUTATED                    1                                 3
  RUFY3 WILD-TYPE                 65                               438
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RUFY3 MUTATED                                       3
  RUFY3 WILD-TYPE                                   158
D44V9, multiclass
                                       clus
vv                                      RUFY3 MUTATED RUFY3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
[1] "Remove cluster labels:" "RUFY3 MUTATED"         
clus
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              1              41 
     TCGA-KL-8324      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433      TCGA-KO-8408 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621      TCGA-B8-5158 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-PJ-A5Z9 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"RUFY3 WILD-TYPE" 
D44V11, continuous
[1] "Remove cluster labels:" "RUFY3 MUTATED"         
clus
  RUFY3 MUTATED RUFY3 WILD-TYPE 
              1              25 
     TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345      TCGA-KM-8639 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409      TCGA-B8-5158 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3472 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117      TCGA-B9-A69E 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6      TCGA-PJ-A5Z9 
"RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" "RUFY3 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"RUFY3 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RUFY3 MUTATED                                  0     0
  RUFY3 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RUFY3 MUTATED                           1     6
  RUFY3 WILD-TYPE                        64   563
D44V12, multiclass
                                  clus
vv                                 RUFY3 MUTATED RUFY3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        6             563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                 cls
clus                0   1
  RUFY3 MUTATED     1   5
  RUFY3 WILD-TYPE  31 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RUFY3 MUTATED      1    5
  RUFY3 WILD-TYPE   31  436
                        clus
vv                       RUFY3 MUTATED RUFY3 WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(45) Variable = PCK1 MUTATION ANALYSIS
D45V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     6   0
  PCK1 WILD-TYPE 480 175
  PCK1 MUTATED PCK1 WILD-TYPE 
             6            655 
  PCK1 MUTATED PCK1 WILD-TYPE 
             0            175 
$`PCK1 MUTATED`
TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 TCGA-CZ-5456 TCGA-AL-3472 
       37.38        66.31         1.94        49.97        56.28        30.35 

$`PCK1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3331 TCGA-A3-3347 
       49.08        49.02        48.59        36.36        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       39.45        59.44        50.24        56.35        47.67        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       58.45        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  PCK1 MUTATED PCK1 WILD-TYPE 
          1.94           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
         66.31         194.79 
  PCK1 MUTATED PCK1 WILD-TYPE 
        43.675         34.190 
[1] "1.9 - 66.3 (43.7)"  "0.1 - 194.8 (34.2)"
[1] "hr="     "3300000"
D45V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         2        2         1        0
  PCK1 WILD-TYPE     325       77       164       86
D45V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              2            325
  STAGE II             2             77
  STAGE III            1            164
  STAGE IV             0             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
  PCK1 MUTATED     2   3   1   0
  PCK1 WILD-TYPE 338  94 220  10
D45V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            2            338
  T2            3             94
  T3            1            220
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  PCK1 MUTATED     4   0   0
  PCK1 WILD-TYPE 268  36   6
D45V5, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  N0            4            268
  N1            0             36
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                cls
clus               0   1
  PCK1 MUTATED     6   0
  PCK1 WILD-TYPE 462  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      6    0
  PCK1 WILD-TYPE  462   78
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            6            462
  1            0             78
[1] 2 2
[1] FALSE
D45V7, binary
                cls
clus               0   1
  PCK1 MUTATED     2   4
  PCK1 WILD-TYPE 227 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    4
  PCK1 WILD-TYPE  227  435
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            2            227
  MALE              4            435
[1] 2 2
[1] FALSE
D45V8, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             78 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411     TCGA-KO-8413     TCGA-AK-3430 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5457     TCGA-CZ-5465 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565     TCGA-DV-5566 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574     TCGA-DV-5575 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905     TCGA-EU-5907 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310     TCGA-A4-8311 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630     TCGA-A4-A4ZT 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  PCK1 MUTATED                    0                                 5
  PCK1 WILD-TYPE                 66                               436
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PCK1 MUTATED                                       1
  PCK1 WILD-TYPE                                   160
D45V9, multiclass
                                       clus
vv                                      PCK1 MUTATED PCK1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                5            436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             41 
    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-B8-4621 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B8-5158     TCGA-B8-5164     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-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7834 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773     TCGA-GL-A59T 
"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-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-PJ-A5Z9 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"PCK1 WILD-TYPE" 
D45V11, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             25 
    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-B8-5158     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117     TCGA-B9-A69E 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"PCK1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PCK1 MUTATED                                  0     0
  PCK1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED                           1     5
  PCK1 WILD-TYPE                        64   564
D45V12, multiclass
                                  clus
vv                                 PCK1 MUTATED PCK1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   1             64
  WHITE                                       5            564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                cls
clus               0   1
  PCK1 MUTATED     0   4
  PCK1 WILD-TYPE  32 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    4
  PCK1 WILD-TYPE   32  437
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            4            437
[1] 2 2
[1] FALSE

Clustering(46) Variable = TXNIP MUTATION ANALYSIS
D46V1, survival
                 sevent
clus2               0   1
  TXNIP MUTATED     4   3
  TXNIP WILD-TYPE 482 172
  TXNIP MUTATED TXNIP WILD-TYPE 
              7             654 
  TXNIP MUTATED TXNIP WILD-TYPE 
              3             172 
$`TXNIP MUTATED`
TCGA-B0-4810 TCGA-BP-4340 TCGA-BP-5201 TCGA-CJ-4869 TCGA-CJ-5684 TCGA-CZ-4866 
       15.72        18.48        31.27        83.97        73.35        61.41 
TCGA-BQ-5889 
       10.88 

$`TXNIP WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 
        3.16        43.96         6.64         3.25        20.25        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 
       27.78        62.07        80.68         0.07        93.99        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       44.55        34.95         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       18.15        61.91        62.10        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  TXNIP MUTATED TXNIP WILD-TYPE 
          10.88            0.07 
  TXNIP MUTATED TXNIP WILD-TYPE 
          83.97          194.79 
  TXNIP MUTATED TXNIP WILD-TYPE 
         31.270          34.325 
[1] "10.9 - 84.0 (31.3)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.5"
D46V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TXNIP MUTATED         2        0         4        2
  TXNIP WILD-TYPE     325       79       161       84
D46V3, multiclass
           clus
vv          TXNIP MUTATED TXNIP WILD-TYPE
  STAGE I               2             325
  STAGE II              0              79
  STAGE III             4             161
  STAGE IV              2              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  TXNIP MUTATED     2   1   5   0
  TXNIP WILD-TYPE 338  96 216  10
D46V4, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  T1             2             338
  T2             1              96
  T3             5             216
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TXNIP MUTATED     2   3   0
  TXNIP WILD-TYPE 270  33   6
D46V5, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  N0             2             270
  N1             3              33
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                 cls
clus                0   1
  TXNIP MUTATED     6   2
  TXNIP WILD-TYPE 462  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      6    2
  TXNIP WILD-TYPE  462   76
   clus
vv  TXNIP MUTATED TXNIP WILD-TYPE
  0             6             462
  1             2              76
[1] 2 2
[1] FALSE
D46V7, binary
                 cls
clus                0   1
  TXNIP MUTATED     3   5
  TXNIP WILD-TYPE 226 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      3    5
  TXNIP WILD-TYPE  226  434
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  FEMALE             3             226
  MALE               5             434
[1] 2 2
[1] FALSE
D46V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TXNIP MUTATED                    0                                 6
  TXNIP WILD-TYPE                 66                               435
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TXNIP MUTATED                                       2
  TXNIP WILD-TYPE                                   159
D46V9, multiclass
                                       clus
vv                                      TXNIP MUTATED TXNIP WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
D46V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TXNIP MUTATED                                  0     0
  TXNIP WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TXNIP MUTATED                           0     7
  TXNIP WILD-TYPE                        65   562
D46V12, multiclass
                                  clus
vv                                 TXNIP MUTATED TXNIP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              65
  WHITE                                        7             562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                 cls
clus                0   1
  TXNIP MUTATED     1   5
  TXNIP WILD-TYPE  31 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      1    5
  TXNIP WILD-TYPE   31  436
                        clus
vv                       TXNIP MUTATED TXNIP WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(47) Variable = RNF128 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  RNF128 MUTATED     3   2
  RNF128 WILD-TYPE 483 173
  RNF128 MUTATED RNF128 WILD-TYPE 
               5              656 
  RNF128 MUTATED RNF128 WILD-TYPE 
               2              173 
$`RNF128 MUTATED`
TCGA-CJ-5672 TCGA-CZ-4861 TCGA-A4-8312 TCGA-B9-4117 TCGA-P4-A5ED 
       72.00        14.66        23.28         0.46        92.58 

$`RNF128 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
        4.57        18.81        63.88        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.97        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 
       12.46        50.50        28.18        26.40        20.61        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-PJ-A5Z8 
       99.78        87.22        42.94         6.61        84.95        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  RNF128 MUTATED RNF128 WILD-TYPE 
            0.46             0.07 
  RNF128 MUTATED RNF128 WILD-TYPE 
           92.58           194.79 
  RNF128 MUTATED RNF128 WILD-TYPE 
          23.280           34.325 
[1] "0.5 - 92.6 (23.3)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "1.5"
D47V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RNF128 MUTATED         3        1         0        0
  RNF128 WILD-TYPE     324       78       165       86
D47V3, multiclass
           clus
vv          RNF128 MUTATED RNF128 WILD-TYPE
  STAGE I                3              324
  STAGE II               1               78
  STAGE III              0              165
  STAGE IV               0               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
  RNF128 MUTATED     3   2   0   0
  RNF128 WILD-TYPE 337  95 221  10
D47V4, multiclass
    clus
vv   RNF128 MUTATED RNF128 WILD-TYPE
  T1              3              337
  T2              2               95
  T3              0              221
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  RNF128 MUTATED     0   0   0
  RNF128 WILD-TYPE 272  36   6
D47V5, multiclass
D47V6, binary
                  cls
clus                 0   1
  RNF128 MUTATED     2   0
  RNF128 WILD-TYPE 466  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      2    0
  RNF128 WILD-TYPE  466   78
   clus
vv  RNF128 MUTATED RNF128 WILD-TYPE
  0              2              466
  1              0               78
[1] 2 2
[1] FALSE
D47V7, binary
                  cls
clus                 0   1
  RNF128 MUTATED     1   4
  RNF128 WILD-TYPE 228 435
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      1    4
  RNF128 WILD-TYPE  228  435
        clus
vv       RNF128 MUTATED RNF128 WILD-TYPE
  FEMALE              1              228
  MALE                4              435
[1] 2 2
[1] FALSE
D47V8, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               2               77 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5465 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT       TCGA-A4-A57E 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793       TCGA-G7-6796 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"RNF128 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RNF128 MUTATED                    0                                 2
  RNF128 WILD-TYPE                 66                               439
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RNF128 MUTATED                                       3
  RNF128 WILD-TYPE                                   158
D47V9, multiclass
                                       clus
vv                                      RNF128 MUTATED RNF128 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               1               41 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-B8-4621 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A48D 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-7268 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"RNF128 WILD-TYPE" 
D47V11, continuous
[1] "Remove cluster labels:" "RNF128 MUTATED"        
clus
  RNF128 MUTATED RNF128 WILD-TYPE 
               1               25 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-B8-5158       TCGA-A4-A48D       TCGA-A4-A57E       TCGA-A4-A5Y0 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-AL-3472       TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-A69E 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-IA-A40U       TCGA-P4-A5E6       TCGA-PJ-A5Z9 
"RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" "RNF128 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"RNF128 WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RNF128 MUTATED                                  0     0
  RNF128 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  RNF128 MUTATED                           2     3
  RNF128 WILD-TYPE                        63   566
D47V12, multiclass
                                  clus
vv                                 RNF128 MUTATED RNF128 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               63
  WHITE                                         3              566
[1] 4 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
  RNF128 MUTATED     1   3
  RNF128 WILD-TYPE  31 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RNF128 MUTATED      1    3
  RNF128 WILD-TYPE   31  438
                        clus
vv                       RNF128 MUTATED RNF128 WILD-TYPE
  HISPANIC OR LATINO                  1               31
  NOT HISPANIC OR LATINO              3              438
[1] 2 2
[1] FALSE

Clustering(48) Variable = ZFYVE26 MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  ZFYVE26 MUTATED     6   3
  ZFYVE26 WILD-TYPE 480 172
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                9               652 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                3               172 
$`ZFYVE26 MUTATED`
TCGA-B0-4697 TCGA-B0-4817 TCGA-B0-4828 TCGA-B2-3924 TCGA-BP-4759 TCGA-BP-4977 
       19.00        33.50        10.09        35.90        77.98        14.93 
TCGA-CW-5588 TCGA-A4-A5XZ TCGA-B9-4115 
       66.31        15.75        26.40 

$`ZFYVE26 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
        3.48        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        52.21        45.07        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 
       36.53        14.93        54.48        29.10        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       61.32        97.41        32.61         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       11.77        10.36        21.57         9.57         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.53        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        53.65        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       85.78        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         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-A5Y0 
       14.33        12.46        16.96         8.48        16.31         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 
       34.49        12.46        50.50        28.18        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
            10.09              0.07 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
            77.98            194.79 
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
           26.400            34.375 
[1] "10.1 - 78.0 (26.4)" "0.1 - 194.8 (34.4)"
[1] "hr=" "1.5"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  ZFYVE26 MUTATED         5        1         1        2
  ZFYVE26 WILD-TYPE     322       78       164       84
D48V3, multiclass
           clus
vv          ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  STAGE I                 5               322
  STAGE II                1                78
  STAGE III               1               164
  STAGE IV                2                84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  ZFYVE26 MUTATED     5   2   2   0
  ZFYVE26 WILD-TYPE 335  95 219  10
D48V4, multiclass
    clus
vv   ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  T1               5               335
  T2               2                95
  T3               2               219
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  ZFYVE26 MUTATED     1   0   0
  ZFYVE26 WILD-TYPE 271  36   6
D48V5, multiclass
[1] "Remove cluster labels:" "ZFYVE26 MUTATED"       
clus
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                1               313 
       TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328        TCGA-KL-8329 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332        TCGA-KL-8333 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336        TCGA-KL-8337 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340        TCGA-KL-8341 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8430        TCGA-KO-8405        TCGA-KO-8406 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8410 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KO-8413        TCGA-KO-8414        TCGA-KO-8415        TCGA-KO-8416 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KO-8417        TCGA-A3-3317        TCGA-A3-3331        TCGA-A3-3347 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3362 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3367        TCGA-A3-3370        TCGA-A3-3373 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A3-3374        TCGA-A3-3376        TCGA-A3-3380        TCGA-A3-3385 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A3-3387        TCGA-AK-3425        TCGA-AK-3427        TCGA-AK-3428 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-AK-3429        TCGA-AK-3430        TCGA-AK-3436        TCGA-AK-3443 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-AK-3450        TCGA-AK-3451        TCGA-AK-3456        TCGA-B0-4690 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4691        TCGA-B0-4693        TCGA-B0-4703        TCGA-B0-4710 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4814        TCGA-B0-4816 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4823        TCGA-B0-4824        TCGA-B0-4827        TCGA-B0-4833 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4837        TCGA-B0-4838        TCGA-B0-4839        TCGA-B0-4842 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4843        TCGA-B0-4846        TCGA-B0-4852        TCGA-B0-4945 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5075        TCGA-B0-5077        TCGA-B0-5080        TCGA-B0-5081 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5083        TCGA-B0-5084        TCGA-B0-5085        TCGA-B0-5088 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5092        TCGA-B0-5094        TCGA-B0-5095        TCGA-B0-5096 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5097        TCGA-B0-5104        TCGA-B0-5106        TCGA-B0-5107 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110        TCGA-B0-5113 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119        TCGA-B0-5120 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400        TCGA-B0-5691 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5692        TCGA-B0-5694        TCGA-B0-5695        TCGA-B0-5696 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699        TCGA-B0-5701 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705        TCGA-B0-5706 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-5707        TCGA-B0-5710        TCGA-B0-5712        TCGA-B0-5713 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B2-5633        TCGA-B2-5641        TCGA-B4-5377        TCGA-B4-5832 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B4-5834        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4148 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-4151        TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4158        TCGA-BP-4159        TCGA-BP-4160 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4165        TCGA-BP-4166 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4169        TCGA-BP-4170        TCGA-BP-4173        TCGA-BP-4174 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4326        TCGA-BP-4329        TCGA-BP-4330        TCGA-BP-4331 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4337        TCGA-BP-4338        TCGA-BP-4340        TCGA-BP-4342 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4343        TCGA-BP-4345        TCGA-BP-4346        TCGA-BP-4351 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4352        TCGA-BP-4354        TCGA-BP-4756        TCGA-BP-4761 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4768        TCGA-BP-4770        TCGA-BP-4771        TCGA-BP-4787 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4795        TCGA-BP-4797        TCGA-BP-4798        TCGA-BP-4799 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4964        TCGA-BP-4967        TCGA-BP-4968 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4974        TCGA-BP-4985 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-4986        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4995 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-5006        TCGA-BP-5007        TCGA-BP-5010        TCGA-BP-5169 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-5182        TCGA-BP-5186        TCGA-BP-5191        TCGA-BP-5198 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BP-5199        TCGA-BP-5201        TCGA-CJ-4636        TCGA-CJ-4638 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4643        TCGA-CJ-4644 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CJ-4868        TCGA-CJ-4869        TCGA-CJ-4872        TCGA-CJ-4873 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CJ-4874        TCGA-CJ-4876        TCGA-CJ-4890        TCGA-CJ-4891 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CJ-4892        TCGA-CJ-4894        TCGA-CJ-4900        TCGA-CJ-4904 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CJ-4918        TCGA-CJ-5678        TCGA-CJ-6030        TCGA-CJ-6033 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5591        TCGA-CW-6087        TCGA-CZ-4854 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4857        TCGA-CZ-4859        TCGA-CZ-4863 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5454        TCGA-CZ-5456 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5984 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5988        TCGA-CZ-5989 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-P4-A5E6        TCGA-P4-A5E8 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-P4-A5EA 
"ZFYVE26 WILD-TYPE" 
D48V6, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED     5   2
  ZFYVE26 WILD-TYPE 463  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED      5    2
  ZFYVE26 WILD-TYPE  463   76
   clus
vv  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  0               5               463
  1               2                76
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED     3   6
  ZFYVE26 WILD-TYPE 226 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED      3    6
  ZFYVE26 WILD-TYPE  226  433
        clus
vv       ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  FEMALE               3               226
  MALE                 6               433
[1] 2 2
[1] FALSE
D48V8, continuous
[1] "Remove cluster labels:" "ZFYVE26 MUTATED"       
clus
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                1                78 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411        TCGA-KO-8413        TCGA-AK-3430 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5834 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B4-5844        TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-4861        TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-CZ-5465        TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-DV-5566        TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-DV-5575        TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-EU-5907        TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A4-8311        TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A4-A4ZT        TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A6HP 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZFYVE26 MUTATED                    0                                 7
  ZFYVE26 WILD-TYPE                 66                               434
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZFYVE26 MUTATED                                       2
  ZFYVE26 WILD-TYPE                                   159
D48V9, multiclass
                                       clus
vv                                      ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   7               434
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
[1] "Remove cluster labels:" "ZFYVE26 MUTATED"       
clus
  ZFYVE26 MUTATED ZFYVE26 WILD-TYPE 
                1                41 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8416        TCGA-B8-4621 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-A4-8310        TCGA-A4-A48D 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-7268 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-DW-7963        TCGA-G7-7501        TCGA-GL-7773        TCGA-GL-A59T 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-IZ-A6M8        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" "ZFYVE26 WILD-TYPE" 
       TCGA-Q2-A5QZ 
"ZFYVE26 WILD-TYPE" 
D48V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZFYVE26 MUTATED                                  0     0
  ZFYVE26 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  ZFYVE26 MUTATED                           1     8
  ZFYVE26 WILD-TYPE                        64   561
D48V12, multiclass
                                  clus
vv                                 ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                64
  WHITE                                          8               561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                  0   1
  ZFYVE26 MUTATED     0   8
  ZFYVE26 WILD-TYPE  32 433
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ZFYVE26 MUTATED      0    8
  ZFYVE26 WILD-TYPE   32  433
                        clus
vv                       ZFYVE26 MUTATED ZFYVE26 WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               8               433
[1] 2 2
[1] FALSE

Clustering(49) Variable = FAM160B2 MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                  0   1
  FAM160B2 MUTATED     2   2
  FAM160B2 WILD-TYPE 484 173
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 4                657 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 2                173 
$`FAM160B2 MUTATED`
TCGA-KM-8441 TCGA-B0-4816 TCGA-CJ-5677 TCGA-A4-7997 
       28.80        45.07        25.71        30.48 

$`FAM160B2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
      151.96        23.28        44.91        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        52.21        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
       63.88        72.00        79.89        84.66        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
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-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       19.56        21.67        24.56         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 
       50.50        28.18        26.40        20.61         0.46        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             25.71               0.07 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             45.07             194.79 
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
             29.64              34.36 
[1] "25.7 - 45.1 (29.6)" "0.1 - 194.8 (34.4)"
[1] "hr=" "2.3"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  FAM160B2 MUTATED         2        1         0        1
  FAM160B2 WILD-TYPE     325       78       165       85
D49V3, multiclass
           clus
vv          FAM160B2 MUTATED FAM160B2 WILD-TYPE
  STAGE I                  2                325
  STAGE II                 1                 78
  STAGE III                0                165
  STAGE IV                 1                 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
  FAM160B2 MUTATED     2   1   1   0
  FAM160B2 WILD-TYPE 338  96 220  10
D49V4, multiclass
    clus
vv   FAM160B2 MUTATED FAM160B2 WILD-TYPE
  T1                2                338
  T2                1                 96
  T3                1                220
  T4                0                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  FAM160B2 MUTATED     1   0   0
  FAM160B2 WILD-TYPE 271  36   6
D49V5, multiclass
[1] "Remove cluster labels:" "FAM160B2 MUTATED"      
clus
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 1                313 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8443         TCGA-KN-8418 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KN-8430         TCGA-KO-8405         TCGA-KO-8406 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8407         TCGA-KO-8408         TCGA-KO-8409 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8410         TCGA-KO-8413         TCGA-KO-8414 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3317         TCGA-A3-3331         TCGA-A3-3347 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3349         TCGA-A3-3357         TCGA-A3-3358 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3367 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3370         TCGA-A3-3373         TCGA-A3-3374 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3376         TCGA-A3-3380         TCGA-A3-3385 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A3-3387         TCGA-AK-3425         TCGA-AK-3427 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3428         TCGA-AK-3429         TCGA-AK-3430 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3436         TCGA-AK-3443         TCGA-AK-3450 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AK-3451         TCGA-AK-3456         TCGA-B0-4690 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4691         TCGA-B0-4693         TCGA-B0-4703 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4710         TCGA-B0-4810         TCGA-B0-4811 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4814         TCGA-B0-4817         TCGA-B0-4823 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4824         TCGA-B0-4827         TCGA-B0-4833 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4837         TCGA-B0-4838         TCGA-B0-4839 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4842         TCGA-B0-4843         TCGA-B0-4846 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-4852         TCGA-B0-4945         TCGA-B0-5075 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5077         TCGA-B0-5080         TCGA-B0-5081 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5083         TCGA-B0-5084         TCGA-B0-5085 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5092         TCGA-B0-5094 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5095         TCGA-B0-5096         TCGA-B0-5097 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5104         TCGA-B0-5106         TCGA-B0-5107 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5108         TCGA-B0-5109         TCGA-B0-5110 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5113         TCGA-B0-5115         TCGA-B0-5116 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5119         TCGA-B0-5120         TCGA-B0-5121 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5691 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5692         TCGA-B0-5694         TCGA-B0-5695 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5698 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5699         TCGA-B0-5701         TCGA-B0-5702 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5703         TCGA-B0-5705         TCGA-B0-5706 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5707         TCGA-B0-5710         TCGA-B0-5712 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B0-5713         TCGA-B2-5633         TCGA-B2-5641 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5832         TCGA-B4-5834 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-4148         TCGA-B8-4151         TCGA-B8-4154 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-4619         TCGA-B8-4620         TCGA-B8-4621 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-B8-5159 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5163         TCGA-B8-5164         TCGA-B8-5165 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5545         TCGA-B8-5546         TCGA-B8-5549 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B8-5550         TCGA-B8-5551         TCGA-B8-5553 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4158         TCGA-BP-4159         TCGA-BP-4160 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4162         TCGA-BP-4163         TCGA-BP-4165 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4166         TCGA-BP-4169         TCGA-BP-4170 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4173         TCGA-BP-4174         TCGA-BP-4326 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4329         TCGA-BP-4330         TCGA-BP-4331 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4337         TCGA-BP-4338         TCGA-BP-4340 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4342         TCGA-BP-4343         TCGA-BP-4345 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4346         TCGA-BP-4351         TCGA-BP-4352 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4354         TCGA-BP-4756         TCGA-BP-4761 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4768         TCGA-BP-4770         TCGA-BP-4771 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4787         TCGA-BP-4795         TCGA-BP-4797 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4798         TCGA-BP-4799         TCGA-BP-4960 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4964         TCGA-BP-4967         TCGA-BP-4968 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4974 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4988 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-4989         TCGA-BP-4995         TCGA-BP-5006 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5007         TCGA-BP-5010         TCGA-BP-5169 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5182         TCGA-BP-5186         TCGA-BP-5191 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BP-5198         TCGA-BP-5199         TCGA-BP-5201 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4638         TCGA-CJ-4639 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4640         TCGA-CJ-4643         TCGA-CJ-4644 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4868         TCGA-CJ-4869         TCGA-CJ-4872 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4873         TCGA-CJ-4874         TCGA-CJ-4876 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4890         TCGA-CJ-4891         TCGA-CJ-4892 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4894         TCGA-CJ-4900         TCGA-CJ-4904 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-4918         TCGA-CJ-5678         TCGA-CJ-6030 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CJ-6033         TCGA-CW-5585         TCGA-CW-5591 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CW-6087         TCGA-CZ-4854         TCGA-CZ-4856 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4859         TCGA-CZ-4863 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5451         TCGA-CZ-5452         TCGA-CZ-5454 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5467         TCGA-CZ-5469 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5470         TCGA-CZ-5984         TCGA-CZ-5985 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5986         TCGA-CZ-5988         TCGA-CZ-5989 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-AL-3466 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-A655         TCGA-B1-A656 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B1-A657         TCGA-B9-7268         TCGA-BQ-5877 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7058 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-G7-6789 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A40Y         TCGA-J7-6720 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-J7-8537         TCGA-P4-A5E6         TCGA-P4-A5E8 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-P4-A5EA 
"FAM160B2 WILD-TYPE" 
D49V6, binary
                    cls
clus                   0   1
  FAM160B2 MUTATED     2   1
  FAM160B2 WILD-TYPE 466  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      2    1
  FAM160B2 WILD-TYPE  466   77
   clus
vv  FAM160B2 MUTATED FAM160B2 WILD-TYPE
  0                2                466
  1                1                 77
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                   0   1
  FAM160B2 MUTATED     2   2
  FAM160B2 WILD-TYPE 227 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      2    2
  FAM160B2 WILD-TYPE  227  437
        clus
vv       FAM160B2 MUTATED FAM160B2 WILD-TYPE
  FEMALE                2                227
  MALE                  2                437
[1] 2 2
[1] FALSE
D49V8, continuous
[1] "Remove cluster labels:" "FAM160B2 MUTATED"      
clus
  FAM160B2 MUTATED FAM160B2 WILD-TYPE 
                 1                 78 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8442         TCGA-KM-8443         TCGA-KM-8476 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KM-8477         TCGA-KM-8639         TCGA-KO-8411 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-KO-8413         TCGA-AK-3430         TCGA-B0-4838 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5832         TCGA-B4-5834 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-CZ-4854 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4861 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5568 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5574         TCGA-DV-5575 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-EU-5907         TCGA-A4-7286         TCGA-A4-7828 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A4ZT 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5DU         TCGA-A4-A5XZ 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-A4-A6HP         TCGA-AL-3466         TCGA-DW-5560 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7837 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-IA-A40U         TCGA-IA-A40X 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-Q2-A5QZ 
"FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" "FAM160B2 WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM160B2 MUTATED                    1                                 2
  FAM160B2 WILD-TYPE                 65                               439
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM160B2 MUTATED                                       1
  FAM160B2 WILD-TYPE                                   160
D49V9, multiclass
                                       clus
vv                                      FAM160B2 MUTATED FAM160B2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                    2                439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
D49V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM160B2 MUTATED                                  0     0
  FAM160B2 WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  FAM160B2 MUTATED                           0     4
  FAM160B2 WILD-TYPE                        65   565
D49V12, multiclass
                                  clus
vv                                 FAM160B2 MUTATED FAM160B2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 11
  BLACK OR AFRICAN AMERICAN                       0                 65
  WHITE                                           4                565
[1] 4 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
  FAM160B2 MUTATED     0   4
  FAM160B2 WILD-TYPE  32 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  FAM160B2 MUTATED      0    4
  FAM160B2 WILD-TYPE   32  437
                        clus
vv                       FAM160B2 MUTATED FAM160B2 WILD-TYPE
  HISPANIC OR LATINO                    0                 32
  NOT HISPANIC OR LATINO                4                437
[1] 2 2
[1] FALSE

Clustering(50) Variable = FAM47A MUTATION ANALYSIS
D50V1, survival
                  sevent
clus2                0   1
  FAM47A MUTATED     3   3
  FAM47A WILD-TYPE 483 172
  FAM47A MUTATED FAM47A WILD-TYPE 
               6              655 
  FAM47A MUTATED FAM47A WILD-TYPE 
               3              172 
$`FAM47A MUTATED`
TCGA-KN-8432 TCGA-BP-4164 TCGA-CJ-4638 TCGA-CZ-4865 TCGA-CZ-5465 TCGA-MH-A560 
        2.50        32.61        14.17         5.46        47.54        30.38 

$`FAM47A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-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-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       63.25        73.22        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       60.59        63.39        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 
       47.01        10.85        10.22        21.76        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       34.29        27.78        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  FAM47A MUTATED FAM47A WILD-TYPE 
            2.50             0.07 
  FAM47A MUTATED FAM47A WILD-TYPE 
           47.54           194.79 
  FAM47A MUTATED FAM47A WILD-TYPE 
          22.275           34.390 
[1] "2.5 - 47.5 (22.3)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "3.5"
D50V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  FAM47A MUTATED         2        1         2        1
  FAM47A WILD-TYPE     325       78       163       85
D50V3, multiclass
           clus
vv          FAM47A MUTATED FAM47A WILD-TYPE
  STAGE I                2              325
  STAGE II               1               78
  STAGE III              2              163
  STAGE IV               1               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
  FAM47A MUTATED     2   1   3   0
  FAM47A WILD-TYPE 338  96 218  10
D50V4, multiclass
    clus
vv   FAM47A MUTATED FAM47A WILD-TYPE
  T1              2              338
  T2              1               96
  T3              3              218
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  FAM47A MUTATED     0   1   0
  FAM47A WILD-TYPE 272  35   6
D50V5, multiclass
[1] "Remove cluster labels:" "FAM47A MUTATED"        
clus
  FAM47A MUTATED FAM47A WILD-TYPE 
               1              313 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       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-8339       TCGA-KL-8340       TCGA-KL-8341 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3429       TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AK-3450       TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5088       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4621       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-4158       TCGA-BP-4159 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4160       TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4331       TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4342       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-4795       TCGA-BP-4797       TCGA-BP-4798 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4799       TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4985       TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BP-5198       TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-4856       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-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B1-A657       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-5888       TCGA-BQ-5889       TCGA-BQ-5890 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-5891       TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-7045       TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-BQ-7058       TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-J7-6720       TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-P4-A5EA 
"FAM47A WILD-TYPE" 
D50V6, binary
                  cls
clus                 0   1
  FAM47A MUTATED     3   1
  FAM47A WILD-TYPE 465  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      3    1
  FAM47A WILD-TYPE  465   77
   clus
vv  FAM47A MUTATED FAM47A WILD-TYPE
  0              3              465
  1              1               77
[1] 2 2
[1] FALSE
D50V7, binary
                  cls
clus                 0   1
  FAM47A MUTATED     5   1
  FAM47A WILD-TYPE 224 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      5    1
  FAM47A WILD-TYPE  224  438
        clus
vv       FAM47A MUTATED FAM47A WILD-TYPE
  FEMALE              5              224
  MALE                1              438
[1] 2 2
[1] FALSE
D50V8, continuous
[1] "Remove cluster labels:" "FAM47A MUTATED"        
clus
  FAM47A MUTATED FAM47A WILD-TYPE 
               1               78 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ 
"FAM47A WILD-TYPE" "FAM47A WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM47A MUTATED                    1                                 4
  FAM47A WILD-TYPE                 65                               437
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM47A MUTATED                                       1
  FAM47A WILD-TYPE                                   160
D50V9, multiclass
                                       clus
vv                                      FAM47A MUTATED FAM47A WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              1              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
D50V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM47A MUTATED                                  0     0
  FAM47A WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  FAM47A MUTATED                           0     5
  FAM47A WILD-TYPE                        65   564
D50V12, multiclass
                                  clus
vv                                 FAM47A MUTATED FAM47A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         5              564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                  cls
clus                 0   1
  FAM47A MUTATED     0   4
  FAM47A WILD-TYPE  32 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47A MUTATED      0    4
  FAM47A WILD-TYPE   32  437
                        clus
vv                       FAM47A MUTATED FAM47A WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              4              437
[1] 2 2
[1] FALSE

Clustering(51) Variable = ATP1A1 MUTATION ANALYSIS
D51V1, survival
                  sevent
clus2                0   1
  ATP1A1 MUTATED     9   1
  ATP1A1 WILD-TYPE 477 174
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
              10              651 
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
               1              174 
$`ATP1A1 MUTATED`
TCGA-BP-4758 TCGA-BP-4994 TCGA-CJ-4638 TCGA-CJ-4875 TCGA-CJ-5682 TCGA-CZ-4863 
       72.59        43.00        14.17        77.36        61.91        63.39 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4114 TCGA-MH-A55Z 
       30.58        34.49        28.18        27.78 

$`ATP1A1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       63.25        73.22        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       18.15        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 
       47.08        69.21        58.75        14.66        60.59         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.09        12.46        50.50        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.97        29.10        34.29        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
           14.17             0.07 
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
           77.36           194.79 
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
          38.745           34.190 
[1] "14.2 - 77.4 (38.7)" "0.1 - 194.8 (34.2)"
[1] "hr=" "3.1"
D51V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ATP1A1 MUTATED         4        1         1        3
  ATP1A1 WILD-TYPE     323       78       164       83
D51V3, multiclass
           clus
vv          ATP1A1 MUTATED ATP1A1 WILD-TYPE
  STAGE I                4              323
  STAGE II               1               78
  STAGE III              1              164
  STAGE IV               3               83
[1] 4 2
[1] 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
  ATP1A1 MUTATED     4   2   4   0
  ATP1A1 WILD-TYPE 336  95 217  10
D51V4, multiclass
    clus
vv   ATP1A1 MUTATED ATP1A1 WILD-TYPE
  T1              4              336
  T2              2               95
  T3              4              217
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ATP1A1 MUTATED     1   1   0
  ATP1A1 WILD-TYPE 271  35   6
D51V5, multiclass
[1] "Remove cluster labels:" "ATP1A1 MUTATED"        
clus
  ATP1A1 MUTATED ATP1A1 WILD-TYPE 
               2              312 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-AK-3429       TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-AK-3450       TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5088       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B8-5159       TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B8-5545       TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B8-5551       TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4160       TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4166       TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4174       TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4331       TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4342       TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4351       TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4761       TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4787       TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4799       TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4968       TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4985       TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-4995       TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-5169       TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BP-5198       TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-5451 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A5Y1 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" "ATP1A1 WILD-TYPE" 
D51V6, binary
                  cls
clus                 0   1
  ATP1A1 MUTATED     5   3
  ATP1A1 WILD-TYPE 463  75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A1 MUTATED      5    3
  ATP1A1 WILD-TYPE  463   75
   clus
vv  ATP1A1 MUTATED ATP1A1 WILD-TYPE
  0              5              463
  1              3               75
[1] 2 2
[1] FALSE
D51V7, binary
                  cls
clus                 0   1
  ATP1A1 MUTATED     2   8
  ATP1A1 WILD-TYPE 227 431
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A1 MUTATED      2    8
  ATP1A1 WILD-TYPE  227  431
        clus
vv       ATP1A1 MUTATED ATP1A1 WILD-TYPE
  FEMALE              2              227
  MALE                8              431
[1] 2 2
[1] FALSE
D51V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ATP1A1 MUTATED                    0                                 6
  ATP1A1 WILD-TYPE                 66                               435
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ATP1A1 MUTATED                                       4
  ATP1A1 WILD-TYPE                                   157
D51V9, multiclass
                                       clus
vv                                      ATP1A1 MUTATED ATP1A1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  6              435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              4              157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
D51V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ATP1A1 MUTATED                                  0     0
  ATP1A1 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ATP1A1 MUTATED                           2     8
  ATP1A1 WILD-TYPE                        63   561
D51V12, multiclass
                                  clus
vv                                 ATP1A1 MUTATED ATP1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               63
  WHITE                                         8              561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                  cls
clus                 0   1
  ATP1A1 MUTATED     0   8
  ATP1A1 WILD-TYPE  32 433
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ATP1A1 MUTATED      0    8
  ATP1A1 WILD-TYPE   32  433
                        clus
vv                       ATP1A1 MUTATED ATP1A1 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              8              433
[1] 2 2
[1] FALSE

Clustering(52) Variable = SH3BP2 MUTATION ANALYSIS
D52V1, survival
                  sevent
clus2                0   1
  SH3BP2 MUTATED     4   0
  SH3BP2 WILD-TYPE 482 175
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               4              657 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               0              175 
$`SH3BP2 MUTATED`
TCGA-B4-5836 TCGA-A4-8311 TCGA-B9-4114 TCGA-BQ-5891 
        4.64        23.97        28.18         0.95 

$`SH3BP2 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 
       21.57         9.57         0.23         1.25         0.53         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       25.64        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        12.46        50.50        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       26.04        25.35        13.25        10.88         7.66        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
            0.95             0.07 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
           28.18           194.79 
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
          14.305           34.390 
[1] "0.9 - 28.2 (14.3)"  "0.1 - 194.8 (34.4)"
[1] "hr="     "1200000"
D52V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SH3BP2 MUTATED         2        0         1        0
  SH3BP2 WILD-TYPE     325       79       164       86
D52V3, multiclass
           clus
vv          SH3BP2 MUTATED SH3BP2 WILD-TYPE
  STAGE I                2              325
  STAGE II               0               79
  STAGE III              1              164
  STAGE IV               0               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
  SH3BP2 MUTATED     2   1   1   0
  SH3BP2 WILD-TYPE 338  96 220  10
D52V4, multiclass
    clus
vv   SH3BP2 MUTATED SH3BP2 WILD-TYPE
  T1              2              338
  T2              1               96
  T3              1              220
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SH3BP2 MUTATED     2   0   0
  SH3BP2 WILD-TYPE 270  36   6
D52V5, multiclass
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               2              312 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3429       TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AK-3450       TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5088       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5838 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B1-A657       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
D52V6, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     2   0
  SH3BP2 WILD-TYPE 466  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      2    0
  SH3BP2 WILD-TYPE  466   78
   clus
vv  SH3BP2 MUTATED SH3BP2 WILD-TYPE
  0              2              466
  1              0               78
[1] 2 2
[1] FALSE
D52V7, binary
                  cls
clus                 0   1
  SH3BP2 MUTATED     2   2
  SH3BP2 WILD-TYPE 227 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      2    2
  SH3BP2 WILD-TYPE  227  437
        clus
vv       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  FEMALE              2              227
  MALE                2              437
[1] 2 2
[1] FALSE
D52V8, continuous
[1] "Remove cluster labels:" "SH3BP2 MUTATED"        
clus
  SH3BP2 MUTATED SH3BP2 WILD-TYPE 
               2               77 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5465 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8312 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT       TCGA-A4-A57E 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP       TCGA-AL-3466 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834       TCGA-DW-7837 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840       TCGA-DW-7841 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901       TCGA-EV-5902 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793       TCGA-G7-6796 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502       TCGA-G7-A4TM 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y       TCGA-J7-8537 
"SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" "SH3BP2 WILD-TYPE" 
      TCGA-Q2-A5QZ 
"SH3BP2 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SH3BP2 MUTATED                    0                                 1
  SH3BP2 WILD-TYPE                 66                               440
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SH3BP2 MUTATED                                       3
  SH3BP2 WILD-TYPE                                   158
D52V9, multiclass
                                       clus
vv                                      SH3BP2 MUTATED SH3BP2 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  1              440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              3              158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SH3BP2 MUTATED                                  0     0
  SH3BP2 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SH3BP2 MUTATED                           1     3
  SH3BP2 WILD-TYPE                        64   566
D52V12, multiclass
                                  clus
vv                                 SH3BP2 MUTATED SH3BP2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               64
  WHITE                                         3              566
[1] 4 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
  SH3BP2 MUTATED     0   4
  SH3BP2 WILD-TYPE  32 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SH3BP2 MUTATED      0    4
  SH3BP2 WILD-TYPE   32  437
                        clus
vv                       SH3BP2 MUTATED SH3BP2 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              4              437
[1] 2 2
[1] FALSE

Clustering(53) Variable = FAM200A MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 482 174
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               656 
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               174 
$`FAM200A MUTATED`
TCGA-B0-4710 TCGA-B8-4154 TCGA-BP-4162 TCGA-BP-4762 TCGA-BP-4775 
        3.16        24.66       101.06        44.15        60.59 

$`FAM200A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
      111.02        85.51        94.72        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.62         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-4782 
       10.82         5.33        61.97        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        69.21        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  FAM200A MUTATED FAM200A WILD-TYPE 
             3.16              0.07 
  FAM200A MUTATED FAM200A WILD-TYPE 
           101.06            194.79 
  FAM200A MUTATED FAM200A WILD-TYPE 
            44.15             34.24 
[1] "3.2 - 101.1 (44.1)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.5"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM200A MUTATED         4        0         1        0
  FAM200A WILD-TYPE     323       79       164       86
D53V3, multiclass
           clus
vv          FAM200A MUTATED FAM200A WILD-TYPE
  STAGE I                 4               323
  STAGE II                0                79
  STAGE III               1               164
  STAGE IV                0                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
  FAM200A MUTATED     4   0   1   0
  FAM200A WILD-TYPE 336  97 220  10
D53V4, multiclass
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  T1               4               336
  T2               0                97
  T3               1               220
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  FAM200A MUTATED     3   0   0
  FAM200A WILD-TYPE 269  36   6
D53V5, multiclass
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  N0               3               269
  N1               0                36
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  FAM200A MUTATED     5   0
  FAM200A WILD-TYPE 463  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      5    0
  FAM200A WILD-TYPE  463   78
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               5               463
  1               0                78
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 225 438
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      4    1
  FAM200A WILD-TYPE  225  438
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  FEMALE               4               225
  MALE                 1               438
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAM200A MUTATED                    0                                 5
  FAM200A WILD-TYPE                 66                               436
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAM200A MUTATED                                       0
  FAM200A WILD-TYPE                                   161
D53V9, multiclass
                                       clus
vv                                      FAM200A MUTATED FAM200A WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   5               436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               0               161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAM200A MUTATED                                  0     0
  FAM200A WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  FAM200A MUTATED                           0     5
  FAM200A WILD-TYPE                        65   564
D53V12, multiclass
                                  clus
vv                                 FAM200A MUTATED FAM200A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      0                65
  WHITE                                          5               564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  FAM200A MUTATED     0   2
  FAM200A WILD-TYPE  32 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      0    2
  FAM200A WILD-TYPE   32  439
                        clus
vv                       FAM200A MUTATED FAM200A WILD-TYPE
  HISPANIC OR LATINO                   0                32
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(54) Variable = RTL1 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  RTL1 MUTATED     2   5
  RTL1 WILD-TYPE 484 170
  RTL1 MUTATED RTL1 WILD-TYPE 
             7            654 
  RTL1 MUTATED RTL1 WILD-TYPE 
             5            170 
$`RTL1 MUTATED`
TCGA-KN-8428 TCGA-KN-8435 TCGA-B0-5095 TCGA-CJ-4902 TCGA-CZ-5461 TCGA-A4-A57E 
       52.27       115.00         8.05        49.97        10.85         8.48 
TCGA-BQ-5882 
       21.63 

$`RTL1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 
       87.12        19.33         2.50        11.21        59.08        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       57.17        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         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        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4903 
       39.45        59.44        50.24        56.35        47.67        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       47.01        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         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-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  RTL1 MUTATED RTL1 WILD-TYPE 
          8.05           0.07 
  RTL1 MUTATED RTL1 WILD-TYPE 
        115.00         194.79 
  RTL1 MUTATED RTL1 WILD-TYPE 
        21.630         34.325 
[1] "8.1 - 115.0 (21.6)" "0.1 - 194.8 (34.3)"
[1] "hr=" "3.1"
D54V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RTL1 MUTATED         0        2         3        2
  RTL1 WILD-TYPE     327       77       162       84
D54V3, multiclass
           clus
vv          RTL1 MUTATED RTL1 WILD-TYPE
  STAGE I              0            327
  STAGE II             2             77
  STAGE III            3            162
  STAGE IV             2             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  RTL1 MUTATED     1   3   3   0
  RTL1 WILD-TYPE 339  94 218  10
D54V4, multiclass
    clus
vv   RTL1 MUTATED RTL1 WILD-TYPE
  T1            1            339
  T2            3             94
  T3            3            218
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  RTL1 MUTATED     4   0   0
  RTL1 WILD-TYPE 268  36   6
D54V5, multiclass
    clus
vv   RTL1 MUTATED RTL1 WILD-TYPE
  N0            4            268
  N1            0             36
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                cls
clus               0   1
  RTL1 MUTATED     3   2
  RTL1 WILD-TYPE 465  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTL1 MUTATED      3    2
  RTL1 WILD-TYPE  465   76
   clus
vv  RTL1 MUTATED RTL1 WILD-TYPE
  0            3            465
  1            2             76
[1] 2 2
[1] FALSE
D54V7, binary
                cls
clus               0   1
  RTL1 MUTATED     0   7
  RTL1 WILD-TYPE 229 432
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTL1 MUTATED      0    7
  RTL1 WILD-TYPE  229  432
        clus
vv       RTL1 MUTATED RTL1 WILD-TYPE
  FEMALE            0            229
  MALE              7            432
[1] 2 2
[1] FALSE
D54V8, continuous
[1] "Remove cluster labels:" "RTL1 MUTATED"          
clus
  RTL1 MUTATED RTL1 WILD-TYPE 
             1             78 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411     TCGA-KO-8413     TCGA-AK-3430 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A5DU     TCGA-A4-A5XZ     TCGA-A4-A6HP 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963     TCGA-EV-5901 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-J7-8537     TCGA-Q2-A5QZ 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RTL1 MUTATED                    2                                 3
  RTL1 WILD-TYPE                 64                               438
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RTL1 MUTATED                                       2
  RTL1 WILD-TYPE                                   159
D54V9, multiclass
                                       clus
vv                                      RTL1 MUTATED RTL1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                3            438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            2            159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
[1] "Remove cluster labels:" "RTL1 MUTATED"          
clus
  RTL1 MUTATED RTL1 WILD-TYPE 
             2             40 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416     TCGA-B8-4621     TCGA-B8-5158 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A5Y0 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268     TCGA-B9-A44B 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7963 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-7773     TCGA-GL-A59T     TCGA-HE-A5NI 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U     TCGA-IZ-A6M8 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
D54V11, continuous
[1] "Remove cluster labels:" "RTL1 MUTATED"          
clus
  RTL1 MUTATED RTL1 WILD-TYPE 
             1             25 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-B8-5158     TCGA-A4-A48D     TCGA-A4-A5Y0     TCGA-AL-3472 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117     TCGA-B9-A69E 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" "RTL1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"RTL1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RTL1 MUTATED                                  0     0
  RTL1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  RTL1 MUTATED                           0     6
  RTL1 WILD-TYPE                        65   563
D54V12, multiclass
                                  clus
vv                                 RTL1 MUTATED RTL1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       6            563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                cls
clus               0   1
  RTL1 MUTATED     0   6
  RTL1 WILD-TYPE  32 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  RTL1 MUTATED      0    6
  RTL1 WILD-TYPE   32  435
                        clus
vv                       RTL1 MUTATED RTL1 WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            6            435
[1] 2 2
[1] FALSE

Clustering(55) Variable = NASP MUTATION ANALYSIS
D55V1, survival
                sevent
clus2              0   1
  NASP MUTATED     2   2
  NASP WILD-TYPE 484 173
  NASP MUTATED NASP WILD-TYPE 
             4            657 
  NASP MUTATED NASP WILD-TYPE 
             2            173 
$`NASP MUTATED`
TCGA-KN-8433 TCGA-KO-8415 TCGA-CJ-5679 TCGA-P4-A5EA 
       11.21        57.17        22.32         6.61 

$`NASP WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       77.85        61.58        63.95        39.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38        48.82        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        43.20        55.76        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       65.52        20.28       109.91        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        99.78        87.22        42.94        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  NASP MUTATED NASP WILD-TYPE 
          6.61           0.07 
  NASP MUTATED NASP WILD-TYPE 
         57.17         194.79 
  NASP MUTATED NASP WILD-TYPE 
        16.765         34.360 
[1] "6.6 - 57.2 (16.8)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "3"  
D55V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NASP MUTATED         1        0         3        0
  NASP WILD-TYPE     326       79       162       86
D55V3, multiclass
           clus
vv          NASP MUTATED NASP WILD-TYPE
  STAGE I              1            326
  STAGE II             0             79
  STAGE III            3            162
  STAGE IV             0             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
  NASP MUTATED     1   0   3   0
  NASP WILD-TYPE 339  97 218  10
D55V4, multiclass
    clus
vv   NASP MUTATED NASP WILD-TYPE
  T1            1            339
  T2            0             97
  T3            3            218
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  NASP MUTATED     1   1   0
  NASP WILD-TYPE 271  35   6
D55V5, multiclass
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             2            312 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8416     TCGA-KO-8417 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362     TCGA-A3-3363 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373     TCGA-A3-3374 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A3-3376     TCGA-A3-3380     TCGA-A3-3385     TCGA-A3-3387 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3425     TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3450 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AK-3451     TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4693     TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4811     TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4823     TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4837     TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-4843     TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5075     TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5692     TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5697     TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B2-5633     TCGA-B2-5641     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-B8-4148 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-4621     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-4158     TCGA-BP-4159     TCGA-BP-4160 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4169     TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4326     TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342 
"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-4795     TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4960     TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-4986     TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5182     TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BP-5199     TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4892     TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CJ-4918     TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-CZ-4856     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-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B1-A657     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-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-BQ-7058     TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
D55V6, binary
                cls
clus               0   1
  NASP MUTATED     2   0
  NASP WILD-TYPE 466  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      2    0
  NASP WILD-TYPE  466   78
   clus
vv  NASP MUTATED NASP WILD-TYPE
  0            2            466
  1            0             78
[1] 2 2
[1] FALSE
D55V7, binary
                cls
clus               0   1
  NASP MUTATED     3   1
  NASP WILD-TYPE 226 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      3    1
  NASP WILD-TYPE  226  438
        clus
vv       NASP MUTATED NASP WILD-TYPE
  FEMALE            3            226
  MALE              1            438
[1] 2 2
[1] FALSE
D55V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NASP MUTATED                    2                                 1
  NASP WILD-TYPE                 64                               440
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NASP MUTATED                                       1
  NASP WILD-TYPE                                   160
D55V9, multiclass
                                       clus
vv                                      NASP MUTATED NASP WILD-TYPE
  KIDNEY CHROMOPHOBE                               2             64
  KIDNEY CLEAR CELL RENAL CARCINOMA                1            440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            1            160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             41 
    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-B8-4621     TCGA-B8-5158 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B8-5164     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-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7834 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773     TCGA-GL-A59T 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-PJ-A5Z9 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-Q2-A5QZ 
"NASP WILD-TYPE" 
D55V11, continuous
[1] "Remove cluster labels:" "NASP MUTATED"          
clus
  NASP MUTATED NASP WILD-TYPE 
             1             25 
    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-B8-5158 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117     TCGA-B9-A69E 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" "NASP WILD-TYPE" 
    TCGA-Q2-A5QZ 
"NASP WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NASP MUTATED                                  0     0
  NASP WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  NASP MUTATED                           0     4
  NASP WILD-TYPE                        65   565
D55V12, multiclass
                                  clus
vv                                 NASP MUTATED NASP WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       4            565
[1] 4 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
  NASP MUTATED     1   3
  NASP WILD-TYPE  31 438
[1] "tbl2"
                cls
clus             [,1] [,2]
  NASP MUTATED      1    3
  NASP WILD-TYPE   31  438
                        clus
vv                       NASP MUTATED NASP WILD-TYPE
  HISPANIC OR LATINO                1             31
  NOT HISPANIC OR LATINO            3            438
[1] 2 2
[1] FALSE

Clustering(56) Variable = RPL7A MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  RPL7A MUTATED     2   1
  RPL7A WILD-TYPE 484 174
  RPL7A MUTATED RPL7A WILD-TYPE 
              3             658 
  RPL7A MUTATED RPL7A WILD-TYPE 
              1             174 
$`RPL7A MUTATED`
TCGA-BQ-5889 TCGA-DW-7841 TCGA-P4-A5EB 
       10.88        14.63        84.95 

$`RPL7A WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  RPL7A MUTATED RPL7A WILD-TYPE 
          10.88            0.07 
  RPL7A MUTATED RPL7A WILD-TYPE 
          84.95          194.79 
  RPL7A MUTATED RPL7A WILD-TYPE 
         14.630          34.325 
[1] "10.9 - 85.0 (14.6)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.4"
D56V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RPL7A MUTATED         2        0         0        1
  RPL7A WILD-TYPE     325       79       165       85
D56V3, multiclass
           clus
vv          RPL7A MUTATED RPL7A WILD-TYPE
  STAGE I               2             325
  STAGE II              0              79
  STAGE III             0             165
  STAGE IV              1              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
  RPL7A MUTATED     2   0   1   0
  RPL7A WILD-TYPE 338  97 220  10
D56V4, multiclass
    clus
vv   RPL7A MUTATED RPL7A WILD-TYPE
  T1             2             338
  T2             0              97
  T3             1             220
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RPL7A MUTATED     0   1   0
  RPL7A WILD-TYPE 272  35   6
D56V5, multiclass
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5088      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-4620      TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5159      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5551      TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4160      TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4331      TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4342      TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4351      TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4761      TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4799      TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4985      TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BP-5198      TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4891      TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-4863      TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5984      TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5989      TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B1-A656      TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-P4-A5EA 
"RPL7A WILD-TYPE" 
D56V6, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   1
  RPL7A WILD-TYPE 468  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    1
  RPL7A WILD-TYPE  468   77
   clus
vv  RPL7A MUTATED RPL7A WILD-TYPE
  0             0             468
  1             1              77
[1] 2 2
[1] FALSE
D56V7, binary
                 cls
clus                0   1
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE 229 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE  229  436
        clus
vv       RPL7A MUTATED RPL7A WILD-TYPE
  FEMALE             0             229
  MALE               3             436
[1] 2 2
[1] FALSE
D56V8, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RPL7A MUTATED                    0                                 0
  RPL7A WILD-TYPE                 66                               441
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RPL7A MUTATED                                       3
  RPL7A WILD-TYPE                                   158
D56V9, multiclass
                                       clus
vv                                      RPL7A MUTATED RPL7A WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 0             441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
[1] "Remove cluster labels:" "RPL7A MUTATED"         
clus
  RPL7A MUTATED RPL7A WILD-TYPE 
              1              41 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B8-5158      TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-GL-A59T      TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-PJ-A5Z9 
"RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" "RPL7A WILD-TYPE" 
     TCGA-Q2-A5QZ 
"RPL7A WILD-TYPE" 
D56V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RPL7A MUTATED                                  0     0
  RPL7A WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RPL7A MUTATED                           1     2
  RPL7A WILD-TYPE                        64   567
D56V12, multiclass
                                  clus
vv                                 RPL7A MUTATED RPL7A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        2             567
[1] 4 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
  RPL7A MUTATED     0   3
  RPL7A WILD-TYPE  32 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL7A MUTATED      0    3
  RPL7A WILD-TYPE   32  438
                        clus
vv                       RPL7A MUTATED RPL7A WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             3             438
[1] 2 2
[1] FALSE

Clustering(57) Variable = UIMC1 MUTATION ANALYSIS
D57V1, survival
                 sevent
clus2               0   1
  UIMC1 MUTATED     4   1
  UIMC1 WILD-TYPE 482 174
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              5             656 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
              1             174 
$`UIMC1 MUTATED`
TCGA-B0-4814 TCGA-B0-5097 TCGA-B8-5162 TCGA-BP-4166 TCGA-B1-A656 
        5.52        21.86         1.18         0.43         0.46 

$`UIMC1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       64.27        54.90        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        9.63        58.45        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
       19.56        21.67        24.56         3.55        16.77         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  UIMC1 MUTATED UIMC1 WILD-TYPE 
           0.43            0.07 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
          21.86          194.79 
  UIMC1 MUTATED UIMC1 WILD-TYPE 
           1.18           34.44 
[1] "0.4 - 21.9 (1.2)"   "0.1 - 194.8 (34.4)"
[1] "hr=" "5.5"
D57V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  UIMC1 MUTATED         1        1         2        1
  UIMC1 WILD-TYPE     326       78       163       85
D57V3, multiclass
           clus
vv          UIMC1 MUTATED UIMC1 WILD-TYPE
  STAGE I               1             326
  STAGE II              1              78
  STAGE III             2             163
  STAGE IV              1              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
  UIMC1 MUTATED     1   1   2   1
  UIMC1 WILD-TYPE 339  96 219   9
D57V4, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  T1             1             339
  T2             1              96
  T3             2             219
  T4             1               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  UIMC1 MUTATED     4   0   0
  UIMC1 WILD-TYPE 268  36   6
D57V5, multiclass
    clus
vv   UIMC1 MUTATED UIMC1 WILD-TYPE
  N0             4             268
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                 cls
clus                0   1
  UIMC1 MUTATED     4   1
  UIMC1 WILD-TYPE 464  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      4    1
  UIMC1 WILD-TYPE  464   77
   clus
vv  UIMC1 MUTATED UIMC1 WILD-TYPE
  0             4             464
  1             1              77
[1] 2 2
[1] FALSE
D57V7, binary
                 cls
clus                0   1
  UIMC1 MUTATED     1   4
  UIMC1 WILD-TYPE 228 435
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      1    4
  UIMC1 WILD-TYPE  228  435
        clus
vv       UIMC1 MUTATED UIMC1 WILD-TYPE
  FEMALE             1             228
  MALE               4             435
[1] 2 2
[1] FALSE
D57V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  UIMC1 MUTATED                    0                                 4
  UIMC1 WILD-TYPE                 66                               437
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  UIMC1 MUTATED                                       1
  UIMC1 WILD-TYPE                                   160
D57V9, multiclass
                                       clus
vv                                      UIMC1 MUTATED UIMC1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 4             437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  UIMC1 MUTATED                                  0     0
  UIMC1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  UIMC1 MUTATED                           0     5
  UIMC1 WILD-TYPE                        65   564
D57V12, multiclass
                                  clus
vv                                 UIMC1 MUTATED UIMC1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              65
  WHITE                                        5             564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                 cls
clus                0   1
  UIMC1 MUTATED     0   4
  UIMC1 WILD-TYPE  32 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  UIMC1 MUTATED      0    4
  UIMC1 WILD-TYPE   32  437
                        clus
vv                       UIMC1 MUTATED UIMC1 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             4             437
[1] 2 2
[1] FALSE

Clustering(58) Variable = TCEB1 MUTATION ANALYSIS
D58V1, survival
                 sevent
clus2               0   1
  TCEB1 MUTATED     3   0
  TCEB1 WILD-TYPE 483 175
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              3             658 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              0             175 
$`TCEB1 MUTATED`
TCGA-B8-5545 TCGA-CJ-4889 TCGA-CZ-4862 
       17.16        63.98        60.59 

$`TCEB1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  TCEB1 MUTATED TCEB1 WILD-TYPE 
          17.16            0.07 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
          63.98          194.79 
  TCEB1 MUTATED TCEB1 WILD-TYPE 
          60.59           34.24 
[1] "17.2 - 64.0 (60.6)" "0.1 - 194.8 (34.2)"
[1] "hr="     "3300000"
D58V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TCEB1 MUTATED         3        0         0        0
  TCEB1 WILD-TYPE     324       79       165       86
D58V3, multiclass
           clus
vv          TCEB1 MUTATED TCEB1 WILD-TYPE
  STAGE I               3             324
  STAGE II              0              79
  STAGE III             0             165
  STAGE IV              0              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
  TCEB1 MUTATED     3   0   0   0
  TCEB1 WILD-TYPE 337  97 221  10
D58V4, multiclass
    clus
vv   TCEB1 MUTATED TCEB1 WILD-TYPE
  T1             3             337
  T2             0              97
  T3             0             221
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TCEB1 MUTATED     1   0   0
  TCEB1 WILD-TYPE 271  36   6
D58V5, multiclass
[1] "Remove cluster labels:" "TCEB1 MUTATED"         
clus
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      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-8339      TCGA-KL-8340      TCGA-KL-8341 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5088      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B8-4620      TCGA-B8-4621      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-4158      TCGA-BP-4159      TCGA-BP-4160 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"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-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-4856      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-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-B1-A657      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-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-P4-A5EA 
"TCEB1 WILD-TYPE" 
D58V6, binary
                 cls
clus                0   1
  TCEB1 MUTATED     3   0
  TCEB1 WILD-TYPE 465  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      3    0
  TCEB1 WILD-TYPE  465   78
   clus
vv  TCEB1 MUTATED TCEB1 WILD-TYPE
  0             3             465
  1             0              78
[1] 2 2
[1] FALSE
D58V7, binary
                 cls
clus                0   1
  TCEB1 MUTATED     1   2
  TCEB1 WILD-TYPE 228 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      1    2
  TCEB1 WILD-TYPE  228  437
        clus
vv       TCEB1 MUTATED TCEB1 WILD-TYPE
  FEMALE             1             228
  MALE               2             437
[1] 2 2
[1] FALSE
D58V8, continuous
[1] "Remove cluster labels:" "TCEB1 MUTATED"         
clus
  TCEB1 MUTATED TCEB1 WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      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-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5465 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      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-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"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-DW-7963      TCGA-EV-5901 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"TCEB1 WILD-TYPE" "TCEB1 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TCEB1 MUTATED                    0                                 3
  TCEB1 WILD-TYPE                 66                               438
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TCEB1 MUTATED                                       0
  TCEB1 WILD-TYPE                                   161
D58V9, multiclass
                                       clus
vv                                      TCEB1 MUTATED TCEB1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             0             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TCEB1 MUTATED                                  0     0
  TCEB1 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TCEB1 MUTATED                           1     2
  TCEB1 WILD-TYPE                        64   567
D58V12, multiclass
                                  clus
vv                                 TCEB1 MUTATED TCEB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        2             567
[1] 4 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
  TCEB1 MUTATED     1   2
  TCEB1 WILD-TYPE  31 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB1 MUTATED      1    2
  TCEB1 WILD-TYPE   31  439
                        clus
vv                       TCEB1 MUTATED TCEB1 WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO             2             439
[1] 2 2
[1] FALSE

Clustering(59) Variable = SFMBT1 MUTATION ANALYSIS
D59V1, survival
                  sevent
clus2                0   1
  SFMBT1 MUTATED     1   2
  SFMBT1 WILD-TYPE 485 173
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
               3              658 
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
               2              173 
$`SFMBT1 MUTATED`
TCGA-B0-5099 TCGA-BP-5004 TCGA-DZ-6133 
       15.95        37.02        51.19 

$`SFMBT1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
        0.46        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
       14.63         3.02        40.77        79.86        80.88        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
           15.95             0.07 
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
           51.19           194.79 
  SFMBT1 MUTATED SFMBT1 WILD-TYPE 
           37.02            34.24 
[1] "15.9 - 51.2 (37.0)" "0.1 - 194.8 (34.2)"
[1] "hr=" "2.9"
D59V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  SFMBT1 MUTATED         2        0         1        0
  SFMBT1 WILD-TYPE     325       79       164       86
D59V3, multiclass
           clus
vv          SFMBT1 MUTATED SFMBT1 WILD-TYPE
  STAGE I                2              325
  STAGE II               0               79
  STAGE III              1              164
  STAGE IV               0               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
  SFMBT1 MUTATED     2   0   1   0
  SFMBT1 WILD-TYPE 338  97 220  10
D59V4, multiclass
    clus
vv   SFMBT1 MUTATED SFMBT1 WILD-TYPE
  T1              2              338
  T2              0               97
  T3              1              220
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  SFMBT1 MUTATED     0   0   0
  SFMBT1 WILD-TYPE 272  36   6
D59V5, multiclass
D59V6, binary
                  cls
clus                 0   1
  SFMBT1 MUTATED     2   0
  SFMBT1 WILD-TYPE 466  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFMBT1 MUTATED      2    0
  SFMBT1 WILD-TYPE  466   78
   clus
vv  SFMBT1 MUTATED SFMBT1 WILD-TYPE
  0              2              466
  1              0               78
[1] 2 2
[1] FALSE
D59V7, binary
                  cls
clus                 0   1
  SFMBT1 MUTATED     2   1
  SFMBT1 WILD-TYPE 227 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFMBT1 MUTATED      2    1
  SFMBT1 WILD-TYPE  227  438
        clus
vv       SFMBT1 MUTATED SFMBT1 WILD-TYPE
  FEMALE              2              227
  MALE                1              438
[1] 2 2
[1] FALSE
D59V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SFMBT1 MUTATED                    0                                 2
  SFMBT1 WILD-TYPE                 66                               439
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SFMBT1 MUTATED                                       1
  SFMBT1 WILD-TYPE                                   160
D59V9, multiclass
                                       clus
vv                                      SFMBT1 MUTATED SFMBT1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              1              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SFMBT1 MUTATED                                  0     0
  SFMBT1 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  SFMBT1 MUTATED                           0     3
  SFMBT1 WILD-TYPE                        65   566
D59V12, multiclass
                                  clus
vv                                 SFMBT1 MUTATED SFMBT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         3              566
[1] 4 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
  SFMBT1 MUTATED     0   1
  SFMBT1 WILD-TYPE  32 440
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SFMBT1 MUTATED      0    1
  SFMBT1 WILD-TYPE   32  440
                        clus
vv                       SFMBT1 MUTATED SFMBT1 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              1              440
[1] 2 2
[1] FALSE

Clustering(60) Variable = SLC16A1 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  SLC16A1 MUTATED     3   0
  SLC16A1 WILD-TYPE 483 175
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                3               658 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                0               175 
$`SLC16A1 MUTATED`
TCGA-B4-5834 TCGA-CJ-5676 TCGA-B3-8121 
        1.25        84.66        12.46 

$`SLC16A1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
       21.57         9.57         0.23         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
       18.81        63.88        72.00        79.89        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       44.61         2.20        19.56        21.67        24.56         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
             1.25              0.07 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
            84.66            194.79 
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
           12.460            34.325 
[1] "1.2 - 84.7 (12.5)"  "0.1 - 194.8 (34.3)"
[1] "hr="     "1200000"
D60V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  SLC16A1 MUTATED         2        0         1        0
  SLC16A1 WILD-TYPE     325       79       164       86
D60V3, multiclass
           clus
vv          SLC16A1 MUTATED SLC16A1 WILD-TYPE
  STAGE I                 2               325
  STAGE II                0                79
  STAGE III               1               164
  STAGE IV                0                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
  SLC16A1 MUTATED     2   0   1   0
  SLC16A1 WILD-TYPE 338  97 220  10
D60V4, multiclass
    clus
vv   SLC16A1 MUTATED SLC16A1 WILD-TYPE
  T1               2               338
  T2               0                97
  T3               1               220
  T4               0                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  SLC16A1 MUTATED     1   0   0
  SLC16A1 WILD-TYPE 271  36   6
D60V5, multiclass
[1] "Remove cluster labels:" "SLC16A1 MUTATED"       
clus
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1               313 
       TCGA-KL-8326        TCGA-KL-8327        TCGA-KL-8328        TCGA-KL-8329 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8330        TCGA-KL-8331        TCGA-KL-8332        TCGA-KL-8333 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8334        TCGA-KL-8335        TCGA-KL-8336        TCGA-KL-8337 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8338        TCGA-KL-8339        TCGA-KL-8340        TCGA-KL-8341 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8342        TCGA-KL-8343        TCGA-KL-8344        TCGA-KL-8345 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KL-8346        TCGA-KM-8438        TCGA-KM-8443        TCGA-KN-8418 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8419        TCGA-KN-8421        TCGA-KN-8422        TCGA-KN-8423 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8424        TCGA-KN-8425        TCGA-KN-8427        TCGA-KN-8428 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KN-8429        TCGA-KN-8430        TCGA-KO-8405        TCGA-KO-8406 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8407        TCGA-KO-8408        TCGA-KO-8409        TCGA-KO-8410 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8413        TCGA-KO-8414        TCGA-KO-8415        TCGA-KO-8416 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KO-8417        TCGA-A3-3317        TCGA-A3-3331        TCGA-A3-3347 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3349        TCGA-A3-3357        TCGA-A3-3358        TCGA-A3-3362 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3363        TCGA-A3-3367        TCGA-A3-3370        TCGA-A3-3373 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3374        TCGA-A3-3376        TCGA-A3-3380        TCGA-A3-3385 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A3-3387        TCGA-AK-3425        TCGA-AK-3427        TCGA-AK-3428 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AK-3429        TCGA-AK-3430        TCGA-AK-3436        TCGA-AK-3443 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AK-3450        TCGA-AK-3451        TCGA-AK-3456        TCGA-B0-4690 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4691        TCGA-B0-4693        TCGA-B0-4703        TCGA-B0-4710 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4810        TCGA-B0-4811        TCGA-B0-4814        TCGA-B0-4816 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4817        TCGA-B0-4823        TCGA-B0-4824        TCGA-B0-4827 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4833        TCGA-B0-4837        TCGA-B0-4838        TCGA-B0-4839 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4842        TCGA-B0-4843        TCGA-B0-4846        TCGA-B0-4852 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4945        TCGA-B0-5075        TCGA-B0-5077        TCGA-B0-5080 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5081        TCGA-B0-5083        TCGA-B0-5084        TCGA-B0-5085 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5088        TCGA-B0-5092        TCGA-B0-5094        TCGA-B0-5095 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5096        TCGA-B0-5097        TCGA-B0-5104        TCGA-B0-5106 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5107        TCGA-B0-5108        TCGA-B0-5109        TCGA-B0-5110 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5113        TCGA-B0-5115        TCGA-B0-5116        TCGA-B0-5119 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5120        TCGA-B0-5121        TCGA-B0-5399        TCGA-B0-5400 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5691        TCGA-B0-5692        TCGA-B0-5694        TCGA-B0-5695 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5696        TCGA-B0-5697        TCGA-B0-5698        TCGA-B0-5699 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5701        TCGA-B0-5702        TCGA-B0-5703        TCGA-B0-5705 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5706        TCGA-B0-5707        TCGA-B0-5710        TCGA-B0-5712 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-5713        TCGA-B2-5633        TCGA-B2-5641        TCGA-B4-5377 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5832        TCGA-B4-5835        TCGA-B4-5836        TCGA-B4-5838 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5843        TCGA-B4-5844        TCGA-B8-4143        TCGA-B8-4148 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-4151        TCGA-B8-4154        TCGA-B8-4619        TCGA-B8-4620 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-4621        TCGA-B8-4622        TCGA-B8-5158        TCGA-B8-5159 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5163        TCGA-B8-5164        TCGA-B8-5165        TCGA-B8-5545 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5546        TCGA-B8-5549        TCGA-B8-5550        TCGA-B8-5551 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B8-5553        TCGA-BP-4158        TCGA-BP-4159        TCGA-BP-4160 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4162        TCGA-BP-4163        TCGA-BP-4165        TCGA-BP-4166 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4169        TCGA-BP-4170        TCGA-BP-4173        TCGA-BP-4174 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4326        TCGA-BP-4329        TCGA-BP-4330        TCGA-BP-4331 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4337        TCGA-BP-4338        TCGA-BP-4340        TCGA-BP-4342 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4343        TCGA-BP-4345        TCGA-BP-4346        TCGA-BP-4351 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4352        TCGA-BP-4354        TCGA-BP-4756        TCGA-BP-4761 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4768        TCGA-BP-4770        TCGA-BP-4771        TCGA-BP-4787 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4795        TCGA-BP-4797        TCGA-BP-4798        TCGA-BP-4799 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4960        TCGA-BP-4964        TCGA-BP-4967        TCGA-BP-4968 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4970        TCGA-BP-4971        TCGA-BP-4974        TCGA-BP-4985 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-4986        TCGA-BP-4988        TCGA-BP-4989        TCGA-BP-4995 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5006        TCGA-BP-5007        TCGA-BP-5010        TCGA-BP-5169 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5182        TCGA-BP-5186        TCGA-BP-5191        TCGA-BP-5198 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BP-5199        TCGA-BP-5201        TCGA-CJ-4636        TCGA-CJ-4638 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4639        TCGA-CJ-4640        TCGA-CJ-4643        TCGA-CJ-4644 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4868        TCGA-CJ-4869        TCGA-CJ-4872        TCGA-CJ-4873 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4874        TCGA-CJ-4876        TCGA-CJ-4890        TCGA-CJ-4891 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4892        TCGA-CJ-4894        TCGA-CJ-4900        TCGA-CJ-4904 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CJ-4918        TCGA-CJ-5678        TCGA-CJ-6030        TCGA-CJ-6033 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CW-5585        TCGA-CW-5591        TCGA-CW-6087        TCGA-CZ-4854 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-4856        TCGA-CZ-4857        TCGA-CZ-4859        TCGA-CZ-4863 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5451        TCGA-CZ-5452        TCGA-CZ-5454        TCGA-CZ-5456 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5467        TCGA-CZ-5469        TCGA-CZ-5470        TCGA-CZ-5984 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5985        TCGA-CZ-5986        TCGA-CZ-5988        TCGA-CZ-5989 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-A4-A57E 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-A5Y1        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-3473 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-A655        TCGA-B1-A656 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B1-A657        TCGA-B9-7268        TCGA-BQ-5877        TCGA-BQ-5878 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DW-7963        TCGA-DZ-6131        TCGA-G7-6789 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-GL-7966        TCGA-GL-A59R        TCGA-IA-A40U        TCGA-IA-A40Y 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-J7-6720        TCGA-J7-8537        TCGA-P4-A5E6        TCGA-P4-A5E8 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-P4-A5EA 
"SLC16A1 WILD-TYPE" 
D60V6, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     2   0
  SLC16A1 WILD-TYPE 466  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      2    0
  SLC16A1 WILD-TYPE  466   78
   clus
vv  SLC16A1 MUTATED SLC16A1 WILD-TYPE
  0               2               466
  1               0                78
[1] 2 2
[1] FALSE
D60V7, binary
                   cls
clus                  0   1
  SLC16A1 MUTATED     1   2
  SLC16A1 WILD-TYPE 228 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      1    2
  SLC16A1 WILD-TYPE  228  437
        clus
vv       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  FEMALE               1               228
  MALE                 2               437
[1] 2 2
[1] FALSE
D60V8, continuous
[1] "Remove cluster labels:" "SLC16A1 MUTATED"       
clus
  SLC16A1 MUTATED SLC16A1 WILD-TYPE 
                1                78 
       TCGA-KM-8438        TCGA-KM-8439        TCGA-KM-8440        TCGA-KM-8441 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KM-8442        TCGA-KM-8443        TCGA-KM-8476        TCGA-KM-8477 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-KM-8639        TCGA-KO-8411        TCGA-KO-8413        TCGA-AK-3430 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B0-4838        TCGA-B4-5377        TCGA-B4-5832        TCGA-B4-5835 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-B4-5836        TCGA-B4-5838        TCGA-B4-5843        TCGA-B4-5844 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-4854        TCGA-CZ-4856        TCGA-CZ-4858        TCGA-CZ-4861 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-4862        TCGA-CZ-5456        TCGA-CZ-5457        TCGA-CZ-5465 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-CZ-5469        TCGA-CZ-5982        TCGA-DV-5565        TCGA-DV-5566 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DV-5568        TCGA-DV-5569        TCGA-DV-5574        TCGA-DV-5575 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DV-5576        TCGA-EU-5904        TCGA-EU-5905        TCGA-EU-5907 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-A4-8310        TCGA-A4-8311 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-8312        TCGA-A4-8518        TCGA-A4-8630        TCGA-A4-A4ZT 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5DU        TCGA-A4-A5XZ        TCGA-A4-A6HP 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DW-7963        TCGA-EV-5901 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-G7-A4TM        TCGA-IA-A40U        TCGA-IA-A40X        TCGA-IA-A40Y 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
       TCGA-J7-8537        TCGA-Q2-A5QZ 
"SLC16A1 WILD-TYPE" "SLC16A1 WILD-TYPE" 
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  SLC16A1 MUTATED                    0                                 2
  SLC16A1 WILD-TYPE                 66                               439
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  SLC16A1 MUTATED                                       1
  SLC16A1 WILD-TYPE                                   160
D60V9, multiclass
                                       clus
vv                                      SLC16A1 MUTATED SLC16A1 WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  SLC16A1 MUTATED                                  0     0
  SLC16A1 WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  SLC16A1 MUTATED                           1     2
  SLC16A1 WILD-TYPE                        64   567
D60V12, multiclass
                                  clus
vv                                 SLC16A1 MUTATED SLC16A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                11
  BLACK OR AFRICAN AMERICAN                      1                64
  WHITE                                          2               567
[1] 4 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
  SLC16A1 MUTATED     1   2
  SLC16A1 WILD-TYPE  31 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A1 MUTATED      1    2
  SLC16A1 WILD-TYPE   31  439
                        clus
vv                       SLC16A1 MUTATED SLC16A1 WILD-TYPE
  HISPANIC OR LATINO                   1                31
  NOT HISPANIC OR LATINO               2               439
[1] 2 2
[1] FALSE

Clustering(61) Variable = PAM MUTATION ANALYSIS
D61V1, survival
               sevent
clus2             0   1
  PAM MUTATED     4   0
  PAM WILD-TYPE 482 175
  PAM MUTATED PAM WILD-TYPE 
            4           657 
  PAM MUTATED PAM WILD-TYPE 
            0           175 
$`PAM MUTATED`
TCGA-B0-5707 TCGA-HE-A5NI TCGA-IA-A40U TCGA-P4-A5E6 
       92.98        11.84        16.80        99.78 

$`PAM WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        96.92        93.34        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
       68.12        13.41        56.75        73.25         5.49        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       20.25        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  PAM MUTATED PAM WILD-TYPE 
        11.84          0.07 
  PAM MUTATED PAM WILD-TYPE 
        99.78        194.79 
  PAM MUTATED PAM WILD-TYPE 
        54.89         34.29 
[1] "11.8 - 99.8 (54.9)" "0.1 - 194.8 (34.3)"
[1] "hr="     "3300000"
D61V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  PAM MUTATED         2        0         2        0
  PAM WILD-TYPE     325       79       163       86
D61V3, multiclass
           clus
vv          PAM MUTATED PAM WILD-TYPE
  STAGE I             2           325
  STAGE II            0            79
  STAGE III           2           163
  STAGE IV            0            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
  PAM MUTATED     3   0   1   0
  PAM WILD-TYPE 337  97 220  10
D61V4, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  T1           3           337
  T2           0            97
  T3           1           220
  T4           0            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus             N0  N1  N2
  PAM MUTATED     2   1   0
  PAM WILD-TYPE 270  35   6
D61V5, multiclass
    clus
vv   PAM MUTATED PAM WILD-TYPE
  N0           2           270
  N1           1            35
  N2           0             6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
               cls
clus              0   1
  PAM MUTATED     2   0
  PAM WILD-TYPE 466  78
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      2    0
  PAM WILD-TYPE  466   78
   clus
vv  PAM MUTATED PAM WILD-TYPE
  0           2           466
  1           0            78
[1] 2 2
[1] FALSE
D61V7, binary
               cls
clus              0   1
  PAM MUTATED     1   3
  PAM WILD-TYPE 228 436
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      1    3
  PAM WILD-TYPE  228  436
        clus
vv       PAM MUTATED PAM WILD-TYPE
  FEMALE           1           228
  MALE             3           436
[1] 2 2
[1] FALSE
D61V8, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            1            78 
   TCGA-KM-8438    TCGA-KM-8439    TCGA-KM-8440    TCGA-KM-8441    TCGA-KM-8442 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8443    TCGA-KM-8476    TCGA-KM-8477    TCGA-KM-8639    TCGA-KO-8411 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KO-8413    TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-B4-5832 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B4-5834    TCGA-B4-5835    TCGA-B4-5836    TCGA-B4-5838    TCGA-B4-5843 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B4-5844    TCGA-CZ-4854    TCGA-CZ-4856    TCGA-CZ-4858    TCGA-CZ-4861 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465    TCGA-CZ-5469 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568    TCGA-DV-5569 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904    TCGA-EU-5905 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-EU-5907    TCGA-A4-7286    TCGA-A4-7828    TCGA-A4-8310    TCGA-A4-8311 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-8312    TCGA-A4-8518    TCGA-A4-8630    TCGA-A4-A4ZT    TCGA-A4-A57E 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A5DU    TCGA-A4-A5XZ    TCGA-A4-A6HP    TCGA-AL-3466    TCGA-DW-5560 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    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-G7-6790    TCGA-G7-6793    TCGA-G7-6796 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-6797    TCGA-G7-7501    TCGA-G7-7502    TCGA-G7-A4TM    TCGA-IA-A40X 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IA-A40Y    TCGA-J7-8537    TCGA-Q2-A5QZ 
"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                               440
               vv
clus            KIDNEY PAPILLARY RENAL CELL CARCINOMA
  PAM MUTATED                                       3
  PAM WILD-TYPE                                   158
D61V9, multiclass
                                       clus
vv                                      PAM MUTATED PAM WILD-TYPE
  KIDNEY CHROMOPHOBE                              0            66
  KIDNEY CLEAR CELL RENAL CARCINOMA               1           440
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           3           158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
[1] "Remove cluster labels:" "PAM MUTATED"           
clus
  PAM MUTATED PAM WILD-TYPE 
            2            40 
   TCGA-KL-8324    TCGA-KL-8330    TCGA-KL-8335    TCGA-KL-8341    TCGA-KL-8345 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KM-8639    TCGA-KN-8428    TCGA-KN-8433    TCGA-KO-8408    TCGA-KO-8409 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-KO-8416    TCGA-B8-4621    TCGA-B8-5158    TCGA-B8-5164    TCGA-A4-8310 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-A4-A48D    TCGA-A4-A57E    TCGA-A4-A5Y0    TCGA-AL-3466    TCGA-AL-3472 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-AL-7173    TCGA-B1-A654    TCGA-B9-4115    TCGA-B9-4117    TCGA-B9-7268 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-B9-A44B    TCGA-B9-A69E    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7963 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-G7-7501    TCGA-GL-7773    TCGA-GL-A59T    TCGA-HE-A5NJ    TCGA-HE-A5NK 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
   TCGA-IZ-A6M8    TCGA-P4-A5E7    TCGA-P4-A5EB    TCGA-PJ-A5Z9    TCGA-Q2-A5QZ 
"PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" "PAM WILD-TYPE" 
D61V11, continuous
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PAM MUTATED                                  0     0
  PAM WILD-TYPE                                2    11
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  PAM MUTATED                           1     2
  PAM WILD-TYPE                        64   567
D61V12, multiclass
                                  clus
vv                                 PAM MUTATED PAM WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             2
  ASIAN                                      0            11
  BLACK OR AFRICAN AMERICAN                  1            64
  WHITE                                      2           567
[1] 4 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
  PAM MUTATED     0   3
  PAM WILD-TYPE  32 438
[1] "tbl2"
               cls
clus            [,1] [,2]
  PAM MUTATED      0    3
  PAM WILD-TYPE   32  438
                        clus
vv                       PAM MUTATED PAM WILD-TYPE
  HISPANIC OR LATINO               0            32
  NOT HISPANIC OR LATINO           3           438
[1] 2 2
[1] FALSE

Clustering(62) Variable = TMCO3 MUTATION ANALYSIS
D62V1, survival
                 sevent
clus2               0   1
  TMCO3 MUTATED     6   1
  TMCO3 WILD-TYPE 480 174
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              7             654 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              1             174 
$`TMCO3 MUTATED`
TCGA-A3-3331 TCGA-B0-5084 TCGA-BP-4176 TCGA-CJ-4643 TCGA-CZ-4859 TCGA-A4-8515 
       48.82         7.30        64.27        58.95        58.75        23.31 
TCGA-DW-5560 
       11.61 

$`TMCO3 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 
       49.08        49.02        48.59        36.36        37.38        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90        34.36        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4644 
       73.22        14.17        75.88        65.69        54.61        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        0.59        47.08        69.21        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        3.91         6.77         4.18        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8517 
       30.48        29.46        25.64        23.97        23.28        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
        3.81        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  TMCO3 MUTATED TMCO3 WILD-TYPE 
           7.30            0.07 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
          64.27          194.79 
  TMCO3 MUTATED TMCO3 WILD-TYPE 
          48.82           34.24 
[1] "7.3 - 64.3 (48.8)"  "0.1 - 194.8 (34.2)"
[1] "hr=" "1.9"
D62V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TMCO3 MUTATED         5        1         0        1
  TMCO3 WILD-TYPE     322       78       165       85
D62V3, multiclass
           clus
vv          TMCO3 MUTATED TMCO3 WILD-TYPE
  STAGE I               5             322
  STAGE II              1              78
  STAGE III             0             165
  STAGE IV              1              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
  TMCO3 MUTATED     5   1   1   0
  TMCO3 WILD-TYPE 335  96 220  10
D62V4, multiclass
    clus
vv   TMCO3 MUTATED TMCO3 WILD-TYPE
  T1             5             335
  T2             1              96
  T3             1             220
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  TMCO3 MUTATED     3   1   0
  TMCO3 WILD-TYPE 269  35   6
D62V5, multiclass
    clus
vv   TMCO3 MUTATED TMCO3 WILD-TYPE
  N0             3             269
  N1             1              35
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                 cls
clus                0   1
  TMCO3 MUTATED     5   1
  TMCO3 WILD-TYPE 463  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      5    1
  TMCO3 WILD-TYPE  463   77
   clus
vv  TMCO3 MUTATED TMCO3 WILD-TYPE
  0             5             463
  1             1              77
[1] 2 2
[1] FALSE
D62V7, binary
                 cls
clus                0   1
  TMCO3 MUTATED     4   3
  TMCO3 WILD-TYPE 225 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      4    3
  TMCO3 WILD-TYPE  225  436
        clus
vv       TMCO3 MUTATED TMCO3 WILD-TYPE
  FEMALE             4             225
  MALE               3             436
[1] 2 2
[1] FALSE
D62V8, continuous
[1] "Remove cluster labels:" "TMCO3 MUTATED"         
clus
  TMCO3 MUTATED TMCO3 WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-8311      TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-A4ZT      TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-DW-5561      TCGA-DW-7834 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"TMCO3 WILD-TYPE" "TMCO3 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  TMCO3 MUTATED                    0                                 5
  TMCO3 WILD-TYPE                 66                               436
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  TMCO3 MUTATED                                       2
  TMCO3 WILD-TYPE                                   159
D62V9, multiclass
                                       clus
vv                                      TMCO3 MUTATED TMCO3 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             2             159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TMCO3 MUTATED                                  1     0
  TMCO3 WILD-TYPE                                1    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  TMCO3 MUTATED                           0     6
  TMCO3 WILD-TYPE                        65   563
D62V12, multiclass
                                  clus
vv                                 TMCO3 MUTATED TMCO3 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             1               1
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              65
  WHITE                                        6             563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                 cls
clus                0   1
  TMCO3 MUTATED     1   4
  TMCO3 WILD-TYPE  31 437
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCO3 MUTATED      1    4
  TMCO3 WILD-TYPE   31  437
                        clus
vv                       TMCO3 MUTATED TMCO3 WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO             4             437
[1] 2 2
[1] FALSE

Clustering(63) Variable = CCDC82 MUTATION ANALYSIS
D63V1, survival
                  sevent
clus2                0   1
  CCDC82 MUTATED     4   2
  CCDC82 WILD-TYPE 482 173
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               6              655 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               2              173 
$`CCDC82 MUTATED`
TCGA-KL-8346 TCGA-B0-4693 TCGA-B0-4714 TCGA-B4-5836 TCGA-B8-4146 TCGA-CJ-5686 
       62.37         2.53         3.25         4.64        16.80        67.00 

$`CCDC82 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         1.41         4.57         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        6.64        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         5.46         0.36         0.23        23.31 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.53        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       54.90        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       61.91        62.10        73.35        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  CCDC82 MUTATED CCDC82 WILD-TYPE 
            2.53             0.07 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
           67.00           194.79 
  CCDC82 MUTATED CCDC82 WILD-TYPE 
           10.72            34.36 
[1] "2.5 - 67.0 (10.7)"  "0.1 - 194.8 (34.4)"
[1] "hr=" "1.9"
D63V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CCDC82 MUTATED         3        1         1        1
  CCDC82 WILD-TYPE     324       78       164       85
D63V3, multiclass
           clus
vv          CCDC82 MUTATED CCDC82 WILD-TYPE
  STAGE I                3              324
  STAGE II               1               78
  STAGE III              1              164
  STAGE IV               1               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
  CCDC82 MUTATED     3   1   2   0
  CCDC82 WILD-TYPE 337  96 219  10
D63V4, multiclass
    clus
vv   CCDC82 MUTATED CCDC82 WILD-TYPE
  T1              3              337
  T2              1               96
  T3              2              219
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  CCDC82 MUTATED     3   0   0
  CCDC82 WILD-TYPE 269  36   6
D63V5, multiclass
    clus
vv   CCDC82 MUTATED CCDC82 WILD-TYPE
  N0              3              269
  N1              0               36
  N2              0                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                  cls
clus                 0   1
  CCDC82 MUTATED     5   1
  CCDC82 WILD-TYPE 463  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC82 MUTATED      5    1
  CCDC82 WILD-TYPE  463   77
   clus
vv  CCDC82 MUTATED CCDC82 WILD-TYPE
  0              5              463
  1              1               77
[1] 2 2
[1] FALSE
D63V7, binary
                  cls
clus                 0   1
  CCDC82 MUTATED     4   2
  CCDC82 WILD-TYPE 225 437
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC82 MUTATED      4    2
  CCDC82 WILD-TYPE  225  437
        clus
vv       CCDC82 MUTATED CCDC82 WILD-TYPE
  FEMALE              4              225
  MALE                2              437
[1] 2 2
[1] FALSE
D63V8, continuous
[1] "Remove cluster labels:" "CCDC82 MUTATED"        
clus
  CCDC82 MUTATED CCDC82 WILD-TYPE 
               1               78 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4861 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457       TCGA-CZ-5465 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565       TCGA-DV-5566 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574       TCGA-DV-5575 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905       TCGA-EU-5907 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310       TCGA-A4-8311 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630       TCGA-A4-A4ZT 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ       TCGA-A4-A6HP 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-DW-7834 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839       TCGA-DW-7840 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963       TCGA-EV-5901 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-EV-5902       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ 
"CCDC82 WILD-TYPE" "CCDC82 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  CCDC82 MUTATED                    1                                 5
  CCDC82 WILD-TYPE                 65                               436
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  CCDC82 MUTATED                                       0
  CCDC82 WILD-TYPE                                   161
D63V9, multiclass
                                       clus
vv                                      CCDC82 MUTATED CCDC82 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  5              436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              0              161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CCDC82 MUTATED                                  0     0
  CCDC82 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CCDC82 MUTATED                           0     6
  CCDC82 WILD-TYPE                        65   563
D63V12, multiclass
                                  clus
vv                                 CCDC82 MUTATED CCDC82 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         6              563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                  cls
clus                 0   1
  CCDC82 MUTATED     0   5
  CCDC82 WILD-TYPE  32 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CCDC82 MUTATED      0    5
  CCDC82 WILD-TYPE   32  436
                        clus
vv                       CCDC82 MUTATED CCDC82 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(64) Variable = NFAT5 MUTATION ANALYSIS
D64V1, survival
                 sevent
clus2               0   1
  NFAT5 MUTATED     6   2
  NFAT5 WILD-TYPE 480 173
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              8             653 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              2             173 
$`NFAT5 MUTATED`
TCGA-KL-8334 TCGA-AK-3431 TCGA-B0-4707 TCGA-B0-4718 TCGA-B0-5106 TCGA-B2-5633 
       96.95        60.92        19.73        20.25        52.54        11.77 
TCGA-CW-6093 TCGA-B9-A5W8 
      103.43         6.81 

$`NFAT5 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        98.33        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       66.31        15.78        68.61        67.20        57.37        46.78 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
       65.10         5.98         2.14         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 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        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 
       70.52        20.94        43.30        11.24        11.90        34.36 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       90.48        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5635 
       32.61        35.90         1.68        12.30        21.30        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        4.18        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        14.86        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 
       25.15        13.68        25.84         6.38       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF 
        3.68        27.65         1.05        12.43        17.95        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       19.99         2.04        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
        0.13        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        17.75        14.07 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
           6.81            0.07 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         103.43          194.79 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         36.395          34.290 
[1] "6.8 - 103.4 (36.4)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.2"
D64V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NFAT5 MUTATED         3        2         3        0
  NFAT5 WILD-TYPE     324       77       162       86
D64V3, multiclass
           clus
vv          NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE I               3             324
  STAGE II              2              77
  STAGE III             3             162
  STAGE IV              0              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
  NFAT5 MUTATED     3   2   3   0
  NFAT5 WILD-TYPE 337  95 218  10
D64V4, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  T1             3             337
  T2             2              95
  T3             3             218
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  NFAT5 MUTATED     3   0   0
  NFAT5 WILD-TYPE 269  36   6
D64V5, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  N0             3             269
  N1             0              36
  N2             0               6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                 cls
clus                0   1
  NFAT5 MUTATED     8   0
  NFAT5 WILD-TYPE 460  78
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      8    0
  NFAT5 WILD-TYPE  460   78
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             8             460
  1             0              78
[1] 2 2
[1] FALSE
D64V7, binary
                 cls
clus                0   1
  NFAT5 MUTATED     2   6
  NFAT5 WILD-TYPE 227 433
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      2    6
  NFAT5 WILD-TYPE  227  433
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             2             227
  MALE               6             433
[1] 2 2
[1] FALSE
D64V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  NFAT5 MUTATED                    1                                 6
  NFAT5 WILD-TYPE                 65                               435
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  NFAT5 MUTATED                                       1
  NFAT5 WILD-TYPE                                   160
D64V9, multiclass
                                       clus
vv                                      NFAT5 MUTATED NFAT5 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 6             435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             1             160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
D64V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NFAT5 MUTATED                                  0     0
  NFAT5 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  NFAT5 MUTATED                           1     7
  NFAT5 WILD-TYPE                        64   562
D64V12, multiclass
                                  clus
vv                                 NFAT5 MUTATED NFAT5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        7             562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                 cls
clus                0   1
  NFAT5 MUTATED     0   7
  NFAT5 WILD-TYPE  32 434
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0    7
  NFAT5 WILD-TYPE   32  434
                        clus
vv                       NFAT5 MUTATED NFAT5 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             7             434
[1] 2 2
[1] FALSE

Clustering(65) Variable = HNF1B MUTATION ANALYSIS
D65V1, survival
                 sevent
clus2               0   1
  HNF1B MUTATED     1   2
  HNF1B WILD-TYPE 485 173
  HNF1B MUTATED HNF1B WILD-TYPE 
              3             658 
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             173 
$`HNF1B MUTATED`
TCGA-KN-8431 TCGA-B0-5694 TCGA-CW-5580 
       19.33        15.78        64.57 

$`HNF1B WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       14.76       112.80        48.89       101.13        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
        7.36        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  HNF1B MUTATED HNF1B WILD-TYPE 
          15.78            0.07 
  HNF1B MUTATED HNF1B WILD-TYPE 
          64.57          194.79 
  HNF1B MUTATED HNF1B WILD-TYPE 
         19.330          34.325 
[1] "15.8 - 64.6 (19.3)" "0.1 - 194.8 (34.3)"
[1] "hr=" "3"  
D65V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  HNF1B MUTATED         0        1         1        1
  HNF1B WILD-TYPE     327       78       164       85
D65V3, multiclass
           clus
vv          HNF1B MUTATED HNF1B WILD-TYPE
  STAGE I               0             327
  STAGE II              1              78
  STAGE III             1             164
  STAGE IV              1              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
  HNF1B MUTATED     0   1   2   0
  HNF1B WILD-TYPE 340  96 219  10
D65V4, multiclass
    clus
vv   HNF1B MUTATED HNF1B WILD-TYPE
  T1             0             340
  T2             1              96
  T3             2             219
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  HNF1B MUTATED     1   0   0
  HNF1B WILD-TYPE 271  36   6
D65V5, multiclass
[1] "Remove cluster labels:" "HNF1B MUTATED"         
clus
  HNF1B MUTATED HNF1B WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3363      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-A3-3380      TCGA-A3-3385 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5088      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-B0-5691      TCGA-B0-5692      TCGA-B0-5695      TCGA-B0-5696 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4621      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-4158      TCGA-BP-4159      TCGA-BP-4160 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342 
"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-4795      TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-4856      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-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B1-A657      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-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-P4-A5EA 
"HNF1B WILD-TYPE" 
D65V6, binary
                 cls
clus                0   1
  HNF1B MUTATED     1   1
  HNF1B WILD-TYPE 467  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      1    1
  HNF1B WILD-TYPE  467   77
   clus
vv  HNF1B MUTATED HNF1B WILD-TYPE
  0             1             467
  1             1              77
[1] 2 2
[1] FALSE
D65V7, binary
                 cls
clus                0   1
  HNF1B MUTATED     2   1
  HNF1B WILD-TYPE 227 438
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      2    1
  HNF1B WILD-TYPE  227  438
        clus
vv       HNF1B MUTATED HNF1B WILD-TYPE
  FEMALE             2             227
  MALE               1             438
[1] 2 2
[1] FALSE
D65V8, continuous
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  HNF1B MUTATED                    1                                 2
  HNF1B WILD-TYPE                 65                               439
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  HNF1B MUTATED                                       0
  HNF1B WILD-TYPE                                   161
D65V9, multiclass
                                       clus
vv                                      HNF1B MUTATED HNF1B WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 2             439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             0             161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
D65V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1B MUTATED                                  0     0
  HNF1B WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1B MUTATED                           0     2
  HNF1B WILD-TYPE                        65   567
D65V12, multiclass
[1] "Remove cluster labels:" "HNF1B MUTATED"         
clus
  HNF1B MUTATED HNF1B WILD-TYPE 
              2             645 
     TCGA-KL-8323      TCGA-KL-8324      TCGA-KL-8325      TCGA-KL-8326 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8327      TCGA-KL-8328      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-8339      TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8418      TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8423      TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8426 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8427      TCGA-KN-8428      TCGA-KN-8429      TCGA-KN-8430 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8432      TCGA-KN-8433      TCGA-KN-8434      TCGA-KN-8435 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KN-8436      TCGA-KN-8437      TCGA-KO-8403      TCGA-KO-8404 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407      TCGA-KO-8408 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8410      TCGA-KO-8411      TCGA-KO-8413 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416      TCGA-KO-8417 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3316      TCGA-A3-3322      TCGA-A3-3323      TCGA-A3-3326 
"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-A3-3358      TCGA-A3-3362      TCGA-A3-3363      TCGA-A3-3365 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373      TCGA-A3-3374 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A3-3376      TCGA-A3-3383      TCGA-A3-3385      TCGA-A3-3387 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428      TCGA-AK-3429 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3430      TCGA-AK-3431      TCGA-AK-3434      TCGA-AK-3436 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3440      TCGA-AK-3443      TCGA-AK-3445      TCGA-AK-3450 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3451      TCGA-AK-3453      TCGA-AK-3454      TCGA-AK-3455 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3456      TCGA-AK-3458      TCGA-AK-3460      TCGA-AK-3461 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AK-3465      TCGA-AS-3777      TCGA-AS-3778      TCGA-B0-4690 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4694      TCGA-B0-4697 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4700      TCGA-B0-4703      TCGA-B0-4706      TCGA-B0-4707 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4710      TCGA-B0-4712      TCGA-B0-4713      TCGA-B0-4714 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4718      TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4813 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4814      TCGA-B0-4815      TCGA-B0-4816      TCGA-B0-4817 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4818      TCGA-B0-4819      TCGA-B0-4822      TCGA-B0-4823 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4824      TCGA-B0-4827      TCGA-B0-4828      TCGA-B0-4833 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4836      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4841      TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4844 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4845      TCGA-B0-4846      TCGA-B0-4847      TCGA-B0-4848 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-4849      TCGA-B0-4852      TCGA-B0-4945      TCGA-B0-5075 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5077      TCGA-B0-5080      TCGA-B0-5081      TCGA-B0-5083 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088      TCGA-B0-5092 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096      TCGA-B0-5097 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5098      TCGA-B0-5099      TCGA-B0-5100      TCGA-B0-5102 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107      TCGA-B0-5108 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113      TCGA-B0-5115 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5116      TCGA-B0-5117      TCGA-B0-5119      TCGA-B0-5120 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5402 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5693      TCGA-B0-5695 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5698      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-B0-5709      TCGA-B0-5710 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B0-5711      TCGA-B0-5712      TCGA-B0-5713      TCGA-B0-5812 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B2-3923      TCGA-B2-3924      TCGA-B2-4098      TCGA-B2-4099 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B2-4101      TCGA-B2-5633      TCGA-B2-5635      TCGA-B2-5641 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4143      TCGA-B8-4146      TCGA-B8-4148      TCGA-B8-4151 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4153      TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5162      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B8-5551      TCGA-B8-5552      TCGA-B8-5553      TCGA-BP-4158 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4159      TCGA-BP-4160      TCGA-BP-4161      TCGA-BP-4162 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4164      TCGA-BP-4165      TCGA-BP-4166 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4167      TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4174      TCGA-BP-4176      TCGA-BP-4177      TCGA-BP-4326 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331      TCGA-BP-4337 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4341      TCGA-BP-4342 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4347 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4349      TCGA-BP-4351      TCGA-BP-4352      TCGA-BP-4354 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4355      TCGA-BP-4756      TCGA-BP-4758      TCGA-BP-4759 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4760      TCGA-BP-4761      TCGA-BP-4762      TCGA-BP-4763 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4765      TCGA-BP-4766      TCGA-BP-4768      TCGA-BP-4770 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4771      TCGA-BP-4774      TCGA-BP-4775      TCGA-BP-4777 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4781      TCGA-BP-4782      TCGA-BP-4787      TCGA-BP-4789 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4790      TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4799      TCGA-BP-4801      TCGA-BP-4803      TCGA-BP-4804 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4807      TCGA-BP-4960      TCGA-BP-4961      TCGA-BP-4962 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4963      TCGA-BP-4964      TCGA-BP-4965      TCGA-BP-4967 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4972 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4973      TCGA-BP-4974      TCGA-BP-4975      TCGA-BP-4976 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4977      TCGA-BP-4981      TCGA-BP-4982      TCGA-BP-4983 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4985      TCGA-BP-4986      TCGA-BP-4987      TCGA-BP-4988 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4989      TCGA-BP-4991      TCGA-BP-4992      TCGA-BP-4993 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-4994      TCGA-BP-4995      TCGA-BP-4998      TCGA-BP-4999 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5000      TCGA-BP-5001      TCGA-BP-5004      TCGA-BP-5006 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5008      TCGA-BP-5009      TCGA-BP-5010 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5168      TCGA-BP-5169      TCGA-BP-5170      TCGA-BP-5173 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5174      TCGA-BP-5175      TCGA-BP-5176      TCGA-BP-5177 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5178      TCGA-BP-5180      TCGA-BP-5181      TCGA-BP-5182 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5183      TCGA-BP-5184      TCGA-BP-5185      TCGA-BP-5186 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5187      TCGA-BP-5189      TCGA-BP-5190      TCGA-BP-5191 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5192      TCGA-BP-5194      TCGA-BP-5195      TCGA-BP-5196 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5198      TCGA-BP-5199      TCGA-BP-5200      TCGA-BP-5201 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BP-5202      TCGA-CJ-4634      TCGA-CJ-4635      TCGA-CJ-4636 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4637      TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4641      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4870      TCGA-CJ-4871      TCGA-CJ-4872 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4875      TCGA-CJ-4876 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4878      TCGA-CJ-4881      TCGA-CJ-4882      TCGA-CJ-4884 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4885      TCGA-CJ-4886      TCGA-CJ-4887      TCGA-CJ-4888 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4889      TCGA-CJ-4890      TCGA-CJ-4891      TCGA-CJ-4892 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4893      TCGA-CJ-4894      TCGA-CJ-4895      TCGA-CJ-4897 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4899      TCGA-CJ-4900      TCGA-CJ-4901      TCGA-CJ-4902 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4903      TCGA-CJ-4904      TCGA-CJ-4905      TCGA-CJ-4907 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4908      TCGA-CJ-4912      TCGA-CJ-4913      TCGA-CJ-4916 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-4918      TCGA-CJ-4920      TCGA-CJ-4923      TCGA-CJ-5671 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-5672      TCGA-CJ-5675      TCGA-CJ-5676      TCGA-CJ-5677 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-5679      TCGA-CJ-5680      TCGA-CJ-5681 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-5682      TCGA-CJ-5683      TCGA-CJ-5684      TCGA-CJ-5686 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-6027      TCGA-CJ-6028      TCGA-CJ-6030      TCGA-CJ-6031 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CJ-6032      TCGA-CJ-6033      TCGA-CW-5581      TCGA-CW-5583 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CW-5585      TCGA-CW-5588      TCGA-CW-5589      TCGA-CW-5591 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CW-6087      TCGA-CW-6090      TCGA-CW-6093      TCGA-CW-6097 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-4853      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4857 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4859      TCGA-CZ-4861      TCGA-CZ-4862 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-4863      TCGA-CZ-4865      TCGA-CZ-4866      TCGA-CZ-5451 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5453      TCGA-CZ-5454      TCGA-CZ-5455 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5458      TCGA-CZ-5459 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5460      TCGA-CZ-5461      TCGA-CZ-5462      TCGA-CZ-5463 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5467      TCGA-CZ-5468      TCGA-CZ-5469      TCGA-CZ-5982 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5984      TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5987 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-CZ-5988      TCGA-CZ-5989      TCGA-DV-5565      TCGA-DV-5566 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5906 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-EU-5907      TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-7583      TCGA-A4-7584      TCGA-A4-7585      TCGA-A4-7732 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-7734      TCGA-A4-7828      TCGA-A4-7915      TCGA-A4-7996 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-7997      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8515      TCGA-A4-8517      TCGA-A4-8518 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-8630      TCGA-A4-A48D      TCGA-A4-A4ZT      TCGA-A4-A57E 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A5Y0      TCGA-A4-A5Y1 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-A4-A6HP      TCGA-AL-3466      TCGA-AL-3467      TCGA-AL-3472 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-AT-A5NU      TCGA-B1-5398 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B1-A47M      TCGA-B1-A47N      TCGA-B1-A654      TCGA-B1-A655 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B1-A656      TCGA-B1-A657      TCGA-B3-3925      TCGA-B3-3926 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B3-4103      TCGA-B3-4104      TCGA-B3-8121      TCGA-B9-4113 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116      TCGA-B9-4117 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B9-5156      TCGA-B9-7268      TCGA-B9-A44B      TCGA-B9-A5W7 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-B9-A5W8      TCGA-B9-A5W9      TCGA-B9-A69E      TCGA-BQ-5875 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5876      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5881      TCGA-BQ-5883      TCGA-BQ-5884 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5885      TCGA-BQ-5886      TCGA-BQ-5887      TCGA-BQ-5888 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-5893      TCGA-BQ-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7053 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7055      TCGA-BQ-7058      TCGA-BQ-7059      TCGA-BQ-7060 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-BQ-7061      TCGA-BQ-7062      TCGA-DW-5560      TCGA-DW-5561 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-DZ-6131      TCGA-DZ-6133      TCGA-DZ-6134      TCGA-EV-5901 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-F9-A4JJ      TCGA-G7-6789 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-GL-6846      TCGA-GL-7773      TCGA-GL-7966 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-GL-8500      TCGA-GL-A4EM      TCGA-GL-A59R      TCGA-GL-A59T 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-IZ-8195 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-IZ-8196      TCGA-IZ-A6M8      TCGA-IZ-A6M9      TCGA-J7-6720 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-J7-8537      TCGA-KV-A6GD      TCGA-KV-A6GE      TCGA-MH-A55W 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-MH-A55Z      TCGA-MH-A560      TCGA-MH-A561      TCGA-MH-A562 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-P4-A5E6      TCGA-P4-A5E7      TCGA-P4-A5E8      TCGA-P4-A5EA 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-P4-A5EB      TCGA-P4-A5ED      TCGA-PJ-A5Z8      TCGA-PJ-A5Z9 
"HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" "HNF1B WILD-TYPE" 
     TCGA-Q2-A5QZ 
"HNF1B WILD-TYPE" 
D65V13, binary
                 cls
clus                0   1
  HNF1B MUTATED     0   2
  HNF1B WILD-TYPE  32 439
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1B MUTATED      0    2
  HNF1B WILD-TYPE   32  439
                        clus
vv                       HNF1B MUTATED HNF1B WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             2             439
[1] 2 2
[1] FALSE

Clustering(66) Variable = OR2L8 MUTATION ANALYSIS
D66V1, survival
                 sevent
clus2               0   1
  OR2L8 MUTATED     4   3
  OR2L8 WILD-TYPE 482 172
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              7             654 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              3             172 
$`OR2L8 MUTATED`
TCGA-CJ-4916 TCGA-CJ-5677 TCGA-CZ-5465 TCGA-BQ-5889 TCGA-DZ-6133 TCGA-EV-5903 
       45.14        25.71        47.54        10.88        51.19        24.89 
TCGA-IZ-8196 
       21.34 

$`OR2L8 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        54.48        38.56         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
       18.81        63.88        72.00        79.89        84.66        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 
        5.49        16.80        19.99         2.04        22.26        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        11.97        29.10        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       30.38        27.65        20.25        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        6.61        84.95        92.58        12.85        17.75        14.07 

  OR2L8 MUTATED OR2L8 WILD-TYPE 
          10.88            0.07 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
          51.19          194.79 
  OR2L8 MUTATED OR2L8 WILD-TYPE 
         25.710          34.325 
[1] "10.9 - 51.2 (25.7)" "0.1 - 194.8 (34.3)"
[1] "hr=" "2"  
D66V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  OR2L8 MUTATED         3        0         2        2
  OR2L8 WILD-TYPE     324       79       163       84
D66V3, multiclass
           clus
vv          OR2L8 MUTATED OR2L8 WILD-TYPE
  STAGE I               3             324
  STAGE II              0              79
  STAGE III             2             163
  STAGE IV              2              84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               T1  T2  T3  T4
  OR2L8 MUTATED     3   0   4   0
  OR2L8 WILD-TYPE 337  97 217  10
D66V4, multiclass
    clus
vv   OR2L8 MUTATED OR2L8 WILD-TYPE
  T1             3             337
  T2             0              97
  T3             4             217
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  OR2L8 MUTATED     0   1   0
  OR2L8 WILD-TYPE 272  35   6
D66V5, multiclass
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              1             313 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5080 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5081      TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5088      TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5096      TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5107      TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5113      TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5120      TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5691      TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5696      TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5701      TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5706      TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-5713      TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B4-5832      TCGA-B4-5834      TCGA-B4-5835      TCGA-B4-5836 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844      TCGA-B8-4143 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B8-4148      TCGA-B8-4151      TCGA-B8-4154      TCGA-B8-4619 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B8-4620      TCGA-B8-4621      TCGA-B8-4622      TCGA-B8-5158 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B8-5159      TCGA-B8-5163      TCGA-B8-5164      TCGA-B8-5165 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B8-5545      TCGA-B8-5546      TCGA-B8-5549      TCGA-B8-5550 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B8-5551      TCGA-B8-5553      TCGA-BP-4158      TCGA-BP-4159 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4160      TCGA-BP-4162      TCGA-BP-4163      TCGA-BP-4165 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4166      TCGA-BP-4169      TCGA-BP-4170      TCGA-BP-4173 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4174      TCGA-BP-4326      TCGA-BP-4329      TCGA-BP-4330 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4331      TCGA-BP-4337      TCGA-BP-4338      TCGA-BP-4340 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4342      TCGA-BP-4343      TCGA-BP-4345      TCGA-BP-4346 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4351      TCGA-BP-4352      TCGA-BP-4354      TCGA-BP-4756 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4761      TCGA-BP-4768      TCGA-BP-4770      TCGA-BP-4771 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4787      TCGA-BP-4795      TCGA-BP-4797      TCGA-BP-4798 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4799      TCGA-BP-4960      TCGA-BP-4964      TCGA-BP-4967 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4968      TCGA-BP-4970      TCGA-BP-4971      TCGA-BP-4974 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4985      TCGA-BP-4986      TCGA-BP-4988      TCGA-BP-4989 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-4995      TCGA-BP-5006      TCGA-BP-5007      TCGA-BP-5010 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-5169      TCGA-BP-5182      TCGA-BP-5186      TCGA-BP-5191 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BP-5198      TCGA-BP-5199      TCGA-BP-5201      TCGA-CJ-4636 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-4638      TCGA-CJ-4639      TCGA-CJ-4640      TCGA-CJ-4643 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-4644      TCGA-CJ-4868      TCGA-CJ-4869      TCGA-CJ-4872 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-4873      TCGA-CJ-4874      TCGA-CJ-4876      TCGA-CJ-4890 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-4891      TCGA-CJ-4892      TCGA-CJ-4894      TCGA-CJ-4900 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-4904      TCGA-CJ-4918      TCGA-CJ-5678      TCGA-CJ-6030 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CJ-6033      TCGA-CW-5585      TCGA-CW-5591      TCGA-CW-6087 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4857      TCGA-CZ-4859 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-4863      TCGA-CZ-5451      TCGA-CZ-5452      TCGA-CZ-5454 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5467      TCGA-CZ-5469      TCGA-CZ-5470 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-5984      TCGA-CZ-5985      TCGA-CZ-5986      TCGA-CZ-5988 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-5989      TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5Y1      TCGA-AL-3466      TCGA-AL-3472 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B1-A655 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B1-A656      TCGA-B1-A657      TCGA-B9-7268      TCGA-BQ-5877 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5890 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-BQ-7058      TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-GL-7966      TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-J7-6720      TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-P4-A5EA 
"OR2L8 WILD-TYPE" 
D66V6, binary
                 cls
clus                0   1
  OR2L8 MUTATED     3   2
  OR2L8 WILD-TYPE 465  76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      3    2
  OR2L8 WILD-TYPE  465   76
   clus
vv  OR2L8 MUTATED OR2L8 WILD-TYPE
  0             3             465
  1             2              76
[1] 2 2
[1] FALSE
D66V7, binary
                 cls
clus                0   1
  OR2L8 MUTATED     4   3
  OR2L8 WILD-TYPE 225 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      4    3
  OR2L8 WILD-TYPE  225  436
        clus
vv       OR2L8 MUTATED OR2L8 WILD-TYPE
  FEMALE             4             225
  MALE               3             436
[1] 2 2
[1] FALSE
D66V8, continuous
[1] "Remove cluster labels:" "OR2L8 MUTATED"         
clus
  OR2L8 MUTATED OR2L8 WILD-TYPE 
              2              77 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B4-5835      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-B4-5844      TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-EV-5902      TCGA-G7-6790      TCGA-G7-6793      TCGA-G7-6796 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502      TCGA-G7-A4TM 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y      TCGA-J7-8537 
"OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" "OR2L8 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"OR2L8 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  OR2L8 MUTATED                    0                                 3
  OR2L8 WILD-TYPE                 66                               438
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  OR2L8 MUTATED                                       4
  OR2L8 WILD-TYPE                                   157
D66V9, multiclass
                                       clus
vv                                      OR2L8 MUTATED OR2L8 WILD-TYPE
  KIDNEY CHROMOPHOBE                                0              66
  KIDNEY CLEAR CELL RENAL CARCINOMA                 3             438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             4             157
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
D66V11, continuous
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  OR2L8 MUTATED                                  0     0
  OR2L8 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  OR2L8 MUTATED                           0     6
  OR2L8 WILD-TYPE                        65   563
D66V12, multiclass
                                  clus
vv                                 OR2L8 MUTATED OR2L8 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    0              65
  WHITE                                        6             563
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                 cls
clus                0   1
  OR2L8 MUTATED     0   5
  OR2L8 WILD-TYPE  32 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OR2L8 MUTATED      0    5
  OR2L8 WILD-TYPE   32  436
                        clus
vv                       OR2L8 MUTATED OR2L8 WILD-TYPE
  HISPANIC OR LATINO                 0              32
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE

Clustering(67) Variable = IDUA MUTATION ANALYSIS
D67V1, survival
                sevent
clus2              0   1
  IDUA MUTATED     4   1
  IDUA WILD-TYPE 482 174
  IDUA MUTATED IDUA WILD-TYPE 
             5            656 
  IDUA MUTATED IDUA WILD-TYPE 
             1            174 
$`IDUA MUTATED`
TCGA-A4-7585 TCGA-BQ-5883 TCGA-G7-6792 TCGA-GL-7773 TCGA-P4-A5EB 
       35.18        40.83        48.62        12.92        84.95 

$`IDUA WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         9.57         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.28        12.99        12.46         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       20.61         0.46        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81         0.16        14.86        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        21.63        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        61.28        50.40        49.84        26.27 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       13.68        25.84         6.38       194.79         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 
       99.78        87.22        42.94         6.61        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  IDUA MUTATED IDUA WILD-TYPE 
         12.92           0.07 
  IDUA MUTATED IDUA WILD-TYPE 
         84.95         194.79 
  IDUA MUTATED IDUA WILD-TYPE 
         40.83          34.09 
[1] "12.9 - 85.0 (40.8)" "0.1 - 194.8 (34.1)"
[1] "hr=" "1.5"
D67V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IDUA MUTATED         4        0         1        0
  IDUA WILD-TYPE     323       79       164       86
D67V3, multiclass
           clus
vv          IDUA MUTATED IDUA WILD-TYPE
  STAGE I              4            323
  STAGE II             0             79
  STAGE III            1            164
  STAGE IV             0             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
  IDUA MUTATED     4   0   1   0
  IDUA WILD-TYPE 336  97 220  10
D67V4, multiclass
    clus
vv   IDUA MUTATED IDUA WILD-TYPE
  T1            4            336
  T2            0             97
  T3            1            220
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  IDUA MUTATED     1   0   0
  IDUA WILD-TYPE 271  36   6
D67V5, multiclass
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1            313 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8406 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KO-8407     TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8410 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KO-8413     TCGA-KO-8414     TCGA-KO-8415     TCGA-KO-8416 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KO-8417     TCGA-A3-3317     TCGA-A3-3331     TCGA-A3-3347 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A3-3349     TCGA-A3-3357     TCGA-A3-3358     TCGA-A3-3362 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A3-3363     TCGA-A3-3367     TCGA-A3-3370     TCGA-A3-3373 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A3-3374     TCGA-A3-3376     TCGA-A3-3380     TCGA-A3-3385 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A3-3387     TCGA-AK-3425     TCGA-AK-3427     TCGA-AK-3428 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AK-3429     TCGA-AK-3430     TCGA-AK-3436     TCGA-AK-3443 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AK-3450     TCGA-AK-3451     TCGA-AK-3456     TCGA-B0-4690 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4691     TCGA-B0-4693     TCGA-B0-4703     TCGA-B0-4710 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4810     TCGA-B0-4811     TCGA-B0-4814     TCGA-B0-4816 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4817     TCGA-B0-4823     TCGA-B0-4824     TCGA-B0-4827 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4833     TCGA-B0-4837     TCGA-B0-4838     TCGA-B0-4839 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4842     TCGA-B0-4843     TCGA-B0-4846     TCGA-B0-4852 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-4945     TCGA-B0-5075     TCGA-B0-5077     TCGA-B0-5080 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5081     TCGA-B0-5083     TCGA-B0-5084     TCGA-B0-5085 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5088     TCGA-B0-5092     TCGA-B0-5094     TCGA-B0-5095 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5096     TCGA-B0-5097     TCGA-B0-5104     TCGA-B0-5106 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5107     TCGA-B0-5108     TCGA-B0-5109     TCGA-B0-5110 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5113     TCGA-B0-5115     TCGA-B0-5116     TCGA-B0-5119 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5120     TCGA-B0-5121     TCGA-B0-5399     TCGA-B0-5400 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5691     TCGA-B0-5692     TCGA-B0-5694     TCGA-B0-5695 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5696     TCGA-B0-5697     TCGA-B0-5698     TCGA-B0-5699 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5701     TCGA-B0-5702     TCGA-B0-5703     TCGA-B0-5705 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5706     TCGA-B0-5707     TCGA-B0-5710     TCGA-B0-5712 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B0-5713     TCGA-B2-5633     TCGA-B2-5641     TCGA-B4-5377 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B4-5832     TCGA-B4-5834     TCGA-B4-5835     TCGA-B4-5836 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B4-5838     TCGA-B4-5843     TCGA-B4-5844     TCGA-B8-4143 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-4148     TCGA-B8-4151     TCGA-B8-4154     TCGA-B8-4619 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-4620     TCGA-B8-4621     TCGA-B8-4622     TCGA-B8-5158 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-5159     TCGA-B8-5163     TCGA-B8-5164     TCGA-B8-5165 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-5545     TCGA-B8-5546     TCGA-B8-5549     TCGA-B8-5550 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-5551     TCGA-B8-5553     TCGA-BP-4158     TCGA-BP-4159 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4160     TCGA-BP-4162     TCGA-BP-4163     TCGA-BP-4165 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4166     TCGA-BP-4169     TCGA-BP-4170     TCGA-BP-4173 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4174     TCGA-BP-4326     TCGA-BP-4329     TCGA-BP-4330 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4331     TCGA-BP-4337     TCGA-BP-4338     TCGA-BP-4340 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4342     TCGA-BP-4343     TCGA-BP-4345     TCGA-BP-4346 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4351     TCGA-BP-4352     TCGA-BP-4354     TCGA-BP-4756 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4761     TCGA-BP-4768     TCGA-BP-4770     TCGA-BP-4771 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4787     TCGA-BP-4795     TCGA-BP-4797     TCGA-BP-4798 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4799     TCGA-BP-4960     TCGA-BP-4964     TCGA-BP-4967 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4968     TCGA-BP-4970     TCGA-BP-4971     TCGA-BP-4974 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4985     TCGA-BP-4986     TCGA-BP-4988     TCGA-BP-4989 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-4995     TCGA-BP-5006     TCGA-BP-5007     TCGA-BP-5010 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-5169     TCGA-BP-5182     TCGA-BP-5186     TCGA-BP-5191 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BP-5198     TCGA-BP-5199     TCGA-BP-5201     TCGA-CJ-4636 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-4638     TCGA-CJ-4639     TCGA-CJ-4640     TCGA-CJ-4643 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-4644     TCGA-CJ-4868     TCGA-CJ-4869     TCGA-CJ-4872 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-4873     TCGA-CJ-4874     TCGA-CJ-4876     TCGA-CJ-4890 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-4891     TCGA-CJ-4892     TCGA-CJ-4894     TCGA-CJ-4900 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-4904     TCGA-CJ-4918     TCGA-CJ-5678     TCGA-CJ-6030 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CJ-6033     TCGA-CW-5585     TCGA-CW-5591     TCGA-CW-6087 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4857     TCGA-CZ-4859 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CZ-4863     TCGA-CZ-5451     TCGA-CZ-5452     TCGA-CZ-5454 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5467     TCGA-CZ-5469     TCGA-CZ-5470 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CZ-5984     TCGA-CZ-5985     TCGA-CZ-5986     TCGA-CZ-5988 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-CZ-5989     TCGA-A4-7583     TCGA-A4-7915     TCGA-A4-A57E 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A4-A5Y1     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B1-A657     TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-BQ-7058     TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-GL-7966     TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-J7-6720     TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-P4-A5EA 
"IDUA WILD-TYPE" 
D67V6, binary
                cls
clus               0   1
  IDUA MUTATED     2   0
  IDUA WILD-TYPE 466  78
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      2    0
  IDUA WILD-TYPE  466   78
   clus
vv  IDUA MUTATED IDUA WILD-TYPE
  0            2            466
  1            0             78
[1] 2 2
[1] FALSE
D67V7, binary
                cls
clus               0   1
  IDUA MUTATED     1   4
  IDUA WILD-TYPE 228 435
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      1    4
  IDUA WILD-TYPE  228  435
        clus
vv       IDUA MUTATED IDUA WILD-TYPE
  FEMALE            1            228
  MALE              4            435
[1] 2 2
[1] FALSE
D67V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  IDUA MUTATED                    0                                 0
  IDUA WILD-TYPE                 66                               441
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  IDUA MUTATED                                       5
  IDUA WILD-TYPE                                   156
D67V9, multiclass
                                       clus
vv                                      IDUA MUTATED IDUA WILD-TYPE
  KIDNEY CHROMOPHOBE                               0             66
  KIDNEY CLEAR CELL RENAL CARCINOMA                0            441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            5            156
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             2             40 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KO-8408     TCGA-KO-8409     TCGA-KO-8416     TCGA-B8-4621 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-5158     TCGA-B8-5164     TCGA-A4-8310     TCGA-A4-A48D 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4115     TCGA-B9-4117 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-7268     TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-A59T 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-PJ-A5Z9     TCGA-Q2-A5QZ 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
D67V11, continuous
[1] "Remove cluster labels:" "IDUA MUTATED"          
clus
  IDUA MUTATED IDUA WILD-TYPE 
             1             25 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B8-5158     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" "IDUA WILD-TYPE" 
    TCGA-Q2-A5QZ 
"IDUA WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IDUA MUTATED                                  0     0
  IDUA WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  IDUA MUTATED                           2     3
  IDUA WILD-TYPE                        63   566
D67V12, multiclass
                                  clus
vv                                 IDUA MUTATED IDUA WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   2             63
  WHITE                                       3            566
[1] 4 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
  IDUA MUTATED     0   4
  IDUA WILD-TYPE  32 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDUA MUTATED      0    4
  IDUA WILD-TYPE   32  437
                        clus
vv                       IDUA MUTATED IDUA WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            4            437
[1] 2 2
[1] FALSE

Clustering(68) Variable = ZC3H18 MUTATION ANALYSIS
D68V1, survival
                  sevent
clus2                0   1
  ZC3H18 MUTATED     6   0
  ZC3H18 WILD-TYPE 480 175
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               6              655 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               0              175 
$`ZC3H18 MUTATED`
TCGA-A3-3387 TCGA-B0-5693 TCGA-BP-4347 TCGA-CW-6090 TCGA-AL-3467 TCGA-B9-4116 
       20.28       101.13        44.94        83.90        58.45        20.61 

$`ZC3H18 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       18.64        28.31        65.52       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
       14.76       112.80        48.89        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4351 
       74.17        62.86        49.84        49.08        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
       74.66         1.35       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 
       18.12         3.91         6.77         4.18        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
        9.63        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       28.18        26.40         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       24.89        10.68         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       17.95        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
        5.49        16.80        19.99         2.04        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       16.34        12.36         0.13        11.97        29.10        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       42.94         6.61        84.95        92.58        12.85        17.75 
TCGA-Q2-A5QZ 
       14.07 

  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
           20.28             0.07 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
          101.13           194.79 
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
          51.695           34.190 
[1] "20.3 - 101.1 (51.7)" "0.1 - 194.8 (34.2)" 
[1] "hr="     "9100000"
D68V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZC3H18 MUTATED         3        0         1        0
  ZC3H18 WILD-TYPE     324       79       164       86
D68V3, multiclass
           clus
vv          ZC3H18 MUTATED ZC3H18 WILD-TYPE
  STAGE I                3              324
  STAGE II               0               79
  STAGE III              1              164
  STAGE IV               0               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
  ZC3H18 MUTATED     4   1   1   0
  ZC3H18 WILD-TYPE 336  96 220  10
D68V4, multiclass
    clus
vv   ZC3H18 MUTATED ZC3H18 WILD-TYPE
  T1              4              336
  T2              1               96
  T3              1              220
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  ZC3H18 MUTATED     1   0   0
  ZC3H18 WILD-TYPE 271  36   6
D68V5, multiclass
[1] "Remove cluster labels:" "ZC3H18 MUTATED"        
clus
  ZC3H18 MUTATED ZC3H18 WILD-TYPE 
               1              313 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-A4-A5Y1       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-B1-A657       TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BQ-5879       TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BQ-5887       TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BQ-5891       TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BQ-7045       TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-BQ-7058       TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-G7-6793       TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-GL-7966       TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-J7-6720       TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8 
"ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" "ZC3H18 WILD-TYPE" 
      TCGA-P4-A5EA 
"ZC3H18 WILD-TYPE" 
D68V6, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     5   0
  ZC3H18 WILD-TYPE 463  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      5    0
  ZC3H18 WILD-TYPE  463   78
   clus
vv  ZC3H18 MUTATED ZC3H18 WILD-TYPE
  0              5              463
  1              0               78
[1] 2 2
[1] FALSE
D68V7, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     3   3
  ZC3H18 WILD-TYPE 226 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      3    3
  ZC3H18 WILD-TYPE  226  436
        clus
vv       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  FEMALE              3              226
  MALE                3              436
[1] 2 2
[1] FALSE
D68V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  ZC3H18 MUTATED                    0                                 4
  ZC3H18 WILD-TYPE                 66                               437
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  ZC3H18 MUTATED                                       2
  ZC3H18 WILD-TYPE                                   159
D68V9, multiclass
                                       clus
vv                                      ZC3H18 MUTATED ZC3H18 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  4              437
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
D68V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ZC3H18 MUTATED                                  0     0
  ZC3H18 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ZC3H18 MUTATED                           1     5
  ZC3H18 WILD-TYPE                        64   564
D68V12, multiclass
                                  clus
vv                                 ZC3H18 MUTATED ZC3H18 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     1               64
  WHITE                                         5              564
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                  cls
clus                 0   1
  ZC3H18 MUTATED     0   5
  ZC3H18 WILD-TYPE  32 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZC3H18 MUTATED      0    5
  ZC3H18 WILD-TYPE   32  436
                        clus
vv                       ZC3H18 MUTATED ZC3H18 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(69) Variable = GAPDHS MUTATION ANALYSIS
D69V1, survival
                  sevent
clus2                0   1
  GAPDHS MUTATED     3   2
  GAPDHS WILD-TYPE 483 173
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               5              656 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               2              173 
$`GAPDHS MUTATED`
TCGA-KN-8423 TCGA-B0-5098 TCGA-CJ-4916 TCGA-A4-A48D TCGA-A4-A5Y1 
       25.91        52.08        45.14        12.46        12.99 

$`GAPDHS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       54.48        38.56         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.28        23.31        19.63        19.73        14.33        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-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 
       58.45        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        10.09        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        2.10        19.23         6.81         0.16        14.86        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
        7.17         3.81        11.61        13.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       19.00        24.89        10.68         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43        17.95        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 
       73.25         5.49        16.80        19.99         2.04        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 
       34.29        27.78        30.38        27.65        20.25        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
       87.22        42.94         6.61        84.95        92.58        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       17.75        14.07 

  GAPDHS MUTATED GAPDHS WILD-TYPE 
           12.46             0.07 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
           52.08           194.79 
  GAPDHS MUTATED GAPDHS WILD-TYPE 
          25.910           34.325 
[1] "12.5 - 52.1 (25.9)" "0.1 - 194.8 (34.3)"
[1] "hr=" "2"  
D69V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GAPDHS MUTATED         3        0         2        0
  GAPDHS WILD-TYPE     324       79       163       86
D69V3, multiclass
           clus
vv          GAPDHS MUTATED GAPDHS WILD-TYPE
  STAGE I                3              324
  STAGE II               0               79
  STAGE III              2              163
  STAGE IV               0               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
  GAPDHS MUTATED     4   0   1   0
  GAPDHS WILD-TYPE 336  97 220  10
D69V4, multiclass
    clus
vv   GAPDHS MUTATED GAPDHS WILD-TYPE
  T1              4              336
  T2              0               97
  T3              1              220
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GAPDHS MUTATED     1   1   0
  GAPDHS WILD-TYPE 271  35   6
D69V5, multiclass
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               2              312 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8424 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428       TCGA-KN-8429 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406       TCGA-KO-8407 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410       TCGA-KO-8413 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416       TCGA-KO-8417 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347       TCGA-A3-3349 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362       TCGA-A3-3363 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373       TCGA-A3-3374 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385       TCGA-A3-3387 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428       TCGA-AK-3429 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443       TCGA-AK-3450 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690       TCGA-B0-4691 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710       TCGA-B0-4810 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816       TCGA-B0-4817 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827       TCGA-B0-4833 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839       TCGA-B0-4842 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852       TCGA-B0-4945 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080       TCGA-B0-5081 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085       TCGA-B0-5088 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095       TCGA-B0-5096 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106       TCGA-B0-5107 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110       TCGA-B0-5113 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119       TCGA-B0-5120 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400       TCGA-B0-5691 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695       TCGA-B0-5696 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699       TCGA-B0-5701 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705       TCGA-B0-5706 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712       TCGA-B0-5713 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377       TCGA-B4-5832 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143       TCGA-B8-4148 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619       TCGA-B8-4620 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158       TCGA-B8-5159 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5163       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4857       TCGA-CZ-4859       TCGA-CZ-4863 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5451       TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5467       TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-CZ-5985       TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-7583       TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
D69V6, binary
                  cls
clus                 0   1
  GAPDHS MUTATED     2   0
  GAPDHS WILD-TYPE 466  78
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      2    0
  GAPDHS WILD-TYPE  466   78
   clus
vv  GAPDHS MUTATED GAPDHS WILD-TYPE
  0              2              466
  1              0               78
[1] 2 2
[1] FALSE
D69V7, binary
                  cls
clus                 0   1
  GAPDHS MUTATED     2   3
  GAPDHS WILD-TYPE 227 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      2    3
  GAPDHS WILD-TYPE  227  436
        clus
vv       GAPDHS MUTATED GAPDHS WILD-TYPE
  FEMALE              2              227
  MALE                3              436
[1] 2 2
[1] FALSE
D69V8, continuous
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GAPDHS MUTATED                    1                                 2
  GAPDHS WILD-TYPE                 65                               439
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GAPDHS MUTATED                                       2
  GAPDHS WILD-TYPE                                   159
D69V9, multiclass
                                       clus
vv                                      GAPDHS MUTATED GAPDHS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 1               65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  2              439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              2              159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               1               41 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KL-8345       TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8416       TCGA-B8-4621 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5158       TCGA-B8-5164       TCGA-A4-8310       TCGA-A4-A57E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-A4-A5Y0       TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-7173 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B1-A654       TCGA-B9-4115       TCGA-B9-4117       TCGA-B9-7268 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B9-A44B       TCGA-B9-A69E       TCGA-DW-5561       TCGA-DW-7834 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773       TCGA-GL-A59T 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-HE-A5NJ       TCGA-HE-A5NK       TCGA-IA-A40U 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-IZ-A6M8       TCGA-P4-A5E7       TCGA-P4-A5EB       TCGA-PJ-A5Z9 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-Q2-A5QZ 
"GAPDHS WILD-TYPE" 
D69V11, continuous
[1] "Remove cluster labels:" "GAPDHS MUTATED"        
clus
  GAPDHS MUTATED GAPDHS WILD-TYPE 
               1               25 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8341       TCGA-KL-8345 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-B8-5158       TCGA-A4-A57E       TCGA-A4-A5Y0       TCGA-AL-3472 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-AL-7173       TCGA-B1-A654       TCGA-B9-4117       TCGA-B9-A69E 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-DW-5561       TCGA-DW-7963       TCGA-G7-7501       TCGA-GL-7773 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-HE-A5NI       TCGA-IA-A40U       TCGA-P4-A5E6       TCGA-PJ-A5Z9 
"GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" "GAPDHS WILD-TYPE" 
      TCGA-Q2-A5QZ 
"GAPDHS WILD-TYPE" 
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GAPDHS MUTATED                                  0     0
  GAPDHS WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GAPDHS MUTATED                           2     3
  GAPDHS WILD-TYPE                        63   566
D69V12, multiclass
                                  clus
vv                                 GAPDHS MUTATED GAPDHS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     2               63
  WHITE                                         3              566
[1] 4 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
  GAPDHS MUTATED     0   5
  GAPDHS WILD-TYPE  32 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAPDHS MUTATED      0    5
  GAPDHS WILD-TYPE   32  436
                        clus
vv                       GAPDHS MUTATED GAPDHS WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              5              436
[1] 2 2
[1] FALSE

Clustering(70) Variable = GPR137 MUTATION ANALYSIS
D70V1, survival
                  sevent
clus2                0   1
  GPR137 MUTATED     3   1
  GPR137 WILD-TYPE 483 174
  GPR137 MUTATED GPR137 WILD-TYPE 
               4              657 
  GPR137 MUTATED GPR137 WILD-TYPE 
               1              174 
$`GPR137 MUTATED`
TCGA-B0-5117 TCGA-B8-5163 TCGA-CZ-4857 TCGA-EV-5902 
       17.59        27.02        47.08        19.00 

$`GPR137 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 
       86.10        77.85        57.17        61.58        63.95        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 
       49.08        49.02        48.59        36.36        37.38        48.82 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        88.37        42.97        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 
       18.64        28.31        65.52        20.28       109.91        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       57.37        46.78        42.08        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 
       43.30        11.24        11.90        34.36         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91        23.74         1.18         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45        46.16         0.59        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       54.90        34.19        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.84         6.38       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        1.05        12.43        17.95        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       29.10        34.29        27.78        30.38        27.65        20.25 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  GPR137 MUTATED GPR137 WILD-TYPE 
           17.59             0.07 
  GPR137 MUTATED GPR137 WILD-TYPE 
           47.08           194.79 
  GPR137 MUTATED GPR137 WILD-TYPE 
           23.01            34.36 
[1] "17.6 - 47.1 (23.0)" "0.1 - 194.8 (34.4)"
[1] "hr=" "1.4"
D70V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  GPR137 MUTATED         2        0         1        1
  GPR137 WILD-TYPE     325       79       164       85
D70V3, multiclass
           clus
vv          GPR137 MUTATED GPR137 WILD-TYPE
  STAGE I                2              325
  STAGE II               0               79
  STAGE III              1              164
  STAGE IV               1               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
  GPR137 MUTATED     2   0   2   0
  GPR137 WILD-TYPE 338  97 219  10
D70V4, multiclass
    clus
vv   GPR137 MUTATED GPR137 WILD-TYPE
  T1              2              338
  T2              0               97
  T3              2              219
  T4              0               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus                N0  N1  N2
  GPR137 MUTATED     2   0   0
  GPR137 WILD-TYPE 270  36   6
D70V5, multiclass
[1] "Remove cluster labels:" "GPR137 MUTATED"        
clus
  GPR137 MUTATED GPR137 WILD-TYPE 
               2              312 
      TCGA-KL-8326       TCGA-KL-8327       TCGA-KL-8328       TCGA-KL-8329 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KL-8330       TCGA-KL-8331       TCGA-KL-8332       TCGA-KL-8333 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KL-8334       TCGA-KL-8335       TCGA-KL-8336       TCGA-KL-8337 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KL-8338       TCGA-KL-8339       TCGA-KL-8340       TCGA-KL-8341 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KL-8342       TCGA-KL-8343       TCGA-KL-8344       TCGA-KL-8345 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KL-8346       TCGA-KM-8438       TCGA-KM-8443       TCGA-KN-8418 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KN-8419       TCGA-KN-8421       TCGA-KN-8422       TCGA-KN-8423 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KN-8424       TCGA-KN-8425       TCGA-KN-8427       TCGA-KN-8428 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KN-8429       TCGA-KN-8430       TCGA-KO-8405       TCGA-KO-8406 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KO-8407       TCGA-KO-8408       TCGA-KO-8409       TCGA-KO-8410 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KO-8413       TCGA-KO-8414       TCGA-KO-8415       TCGA-KO-8416 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KO-8417       TCGA-A3-3317       TCGA-A3-3331       TCGA-A3-3347 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A3-3349       TCGA-A3-3357       TCGA-A3-3358       TCGA-A3-3362 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A3-3363       TCGA-A3-3367       TCGA-A3-3370       TCGA-A3-3373 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A3-3374       TCGA-A3-3376       TCGA-A3-3380       TCGA-A3-3385 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A3-3387       TCGA-AK-3425       TCGA-AK-3427       TCGA-AK-3428 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-AK-3429       TCGA-AK-3430       TCGA-AK-3436       TCGA-AK-3443 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-AK-3450       TCGA-AK-3451       TCGA-AK-3456       TCGA-B0-4690 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4691       TCGA-B0-4693       TCGA-B0-4703       TCGA-B0-4710 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4810       TCGA-B0-4811       TCGA-B0-4814       TCGA-B0-4816 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4817       TCGA-B0-4823       TCGA-B0-4824       TCGA-B0-4827 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4833       TCGA-B0-4837       TCGA-B0-4838       TCGA-B0-4839 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4842       TCGA-B0-4843       TCGA-B0-4846       TCGA-B0-4852 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4945       TCGA-B0-5075       TCGA-B0-5077       TCGA-B0-5080 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5081       TCGA-B0-5083       TCGA-B0-5084       TCGA-B0-5085 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5088       TCGA-B0-5092       TCGA-B0-5094       TCGA-B0-5095 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5096       TCGA-B0-5097       TCGA-B0-5104       TCGA-B0-5106 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5107       TCGA-B0-5108       TCGA-B0-5109       TCGA-B0-5110 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5113       TCGA-B0-5115       TCGA-B0-5116       TCGA-B0-5119 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5120       TCGA-B0-5121       TCGA-B0-5399       TCGA-B0-5400 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5691       TCGA-B0-5692       TCGA-B0-5694       TCGA-B0-5695 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5696       TCGA-B0-5697       TCGA-B0-5698       TCGA-B0-5699 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5701       TCGA-B0-5702       TCGA-B0-5703       TCGA-B0-5705 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5706       TCGA-B0-5707       TCGA-B0-5710       TCGA-B0-5712 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-5713       TCGA-B2-5633       TCGA-B2-5641       TCGA-B4-5377 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B4-5832       TCGA-B4-5834       TCGA-B4-5835       TCGA-B4-5836 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B4-5838       TCGA-B4-5843       TCGA-B4-5844       TCGA-B8-4143 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B8-4148       TCGA-B8-4151       TCGA-B8-4154       TCGA-B8-4619 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B8-4620       TCGA-B8-4621       TCGA-B8-4622       TCGA-B8-5158 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B8-5159       TCGA-B8-5164       TCGA-B8-5165       TCGA-B8-5545 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B8-5546       TCGA-B8-5549       TCGA-B8-5550       TCGA-B8-5551 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B8-5553       TCGA-BP-4158       TCGA-BP-4159       TCGA-BP-4160 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4162       TCGA-BP-4163       TCGA-BP-4165       TCGA-BP-4166 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4169       TCGA-BP-4170       TCGA-BP-4173       TCGA-BP-4174 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4326       TCGA-BP-4329       TCGA-BP-4330       TCGA-BP-4331 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4337       TCGA-BP-4338       TCGA-BP-4340       TCGA-BP-4342 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4343       TCGA-BP-4345       TCGA-BP-4346       TCGA-BP-4351 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4352       TCGA-BP-4354       TCGA-BP-4756       TCGA-BP-4761 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4768       TCGA-BP-4770       TCGA-BP-4771       TCGA-BP-4787 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4795       TCGA-BP-4797       TCGA-BP-4798       TCGA-BP-4799 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4960       TCGA-BP-4964       TCGA-BP-4967       TCGA-BP-4968 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4970       TCGA-BP-4971       TCGA-BP-4974       TCGA-BP-4985 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-4986       TCGA-BP-4988       TCGA-BP-4989       TCGA-BP-4995 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-5006       TCGA-BP-5007       TCGA-BP-5010       TCGA-BP-5169 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-5182       TCGA-BP-5186       TCGA-BP-5191       TCGA-BP-5198 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BP-5199       TCGA-BP-5201       TCGA-CJ-4636       TCGA-CJ-4638 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CJ-4639       TCGA-CJ-4640       TCGA-CJ-4643       TCGA-CJ-4644 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CJ-4868       TCGA-CJ-4869       TCGA-CJ-4872       TCGA-CJ-4873 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CJ-4874       TCGA-CJ-4876       TCGA-CJ-4890       TCGA-CJ-4891 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CJ-4892       TCGA-CJ-4894       TCGA-CJ-4900       TCGA-CJ-4904 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CJ-4918       TCGA-CJ-5678       TCGA-CJ-6030       TCGA-CJ-6033 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CW-5585       TCGA-CW-5591       TCGA-CW-6087       TCGA-CZ-4854 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4859       TCGA-CZ-4863       TCGA-CZ-5451 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-5452       TCGA-CZ-5454       TCGA-CZ-5456       TCGA-CZ-5467 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-5469       TCGA-CZ-5470       TCGA-CZ-5984       TCGA-CZ-5985 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-5986       TCGA-CZ-5988       TCGA-CZ-5989       TCGA-A4-7583 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A4-7585       TCGA-A4-7915       TCGA-A4-A57E       TCGA-A4-A5Y1 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-AL-3466       TCGA-AL-3472       TCGA-AL-3473       TCGA-AL-7173 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B1-5398       TCGA-B1-A655       TCGA-B1-A656       TCGA-B1-A657 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B9-7268       TCGA-BQ-5877       TCGA-BQ-5878       TCGA-BQ-5879 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BQ-5880       TCGA-BQ-5882       TCGA-BQ-5885       TCGA-BQ-5887 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BQ-5888       TCGA-BQ-5889       TCGA-BQ-5890       TCGA-BQ-5891 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BQ-5892       TCGA-BQ-5893       TCGA-BQ-5894       TCGA-BQ-7045 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-BQ-7048       TCGA-BQ-7050       TCGA-BQ-7051       TCGA-BQ-7058 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-DW-7963       TCGA-DZ-6131       TCGA-G7-6789       TCGA-G7-6793 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-G7-6795       TCGA-G7-7501       TCGA-GL-6846       TCGA-GL-7966 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-GL-A59R       TCGA-IA-A40U       TCGA-IA-A40Y       TCGA-J7-6720 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-J7-8537       TCGA-P4-A5E6       TCGA-P4-A5E8       TCGA-P4-A5EA 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
D70V6, binary
                  cls
clus                 0   1
  GPR137 MUTATED     3   1
  GPR137 WILD-TYPE 465  77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR137 MUTATED      3    1
  GPR137 WILD-TYPE  465   77
   clus
vv  GPR137 MUTATED GPR137 WILD-TYPE
  0              3              465
  1              1               77
[1] 2 2
[1] FALSE
D70V7, binary
                  cls
clus                 0   1
  GPR137 MUTATED     1   3
  GPR137 WILD-TYPE 228 436
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR137 MUTATED      1    3
  GPR137 WILD-TYPE  228  436
        clus
vv       GPR137 MUTATED GPR137 WILD-TYPE
  FEMALE              1              228
  MALE                3              436
[1] 2 2
[1] FALSE
D70V8, continuous
[1] "Remove cluster labels:" "GPR137 MUTATED"        
clus
  GPR137 MUTATED GPR137 WILD-TYPE 
               1               78 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8476       TCGA-KM-8477 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KO-8411       TCGA-KO-8413       TCGA-AK-3430 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B0-4838       TCGA-B4-5377       TCGA-B4-5832       TCGA-B4-5834 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B4-5835       TCGA-B4-5836       TCGA-B4-5838       TCGA-B4-5843 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-B4-5844       TCGA-CZ-4854       TCGA-CZ-4856       TCGA-CZ-4858 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-4861       TCGA-CZ-4862       TCGA-CZ-5456       TCGA-CZ-5457 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982       TCGA-DV-5565 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569       TCGA-DV-5574 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-DV-5575       TCGA-DV-5576       TCGA-EU-5904       TCGA-EU-5905 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-EU-5907       TCGA-A4-7286       TCGA-A4-7828       TCGA-A4-8310 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A4-8311       TCGA-A4-8312       TCGA-A4-8518       TCGA-A4-8630 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A4-A4ZT       TCGA-A4-A57E       TCGA-A4-A5DU       TCGA-A4-A5XZ 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-A4-A6HP       TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-DW-7834       TCGA-DW-7837       TCGA-DW-7838       TCGA-DW-7839 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-DW-7840       TCGA-DW-7841       TCGA-DW-7842       TCGA-DW-7963 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-EV-5901       TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-G7-6796       TCGA-G7-6797       TCGA-G7-7501       TCGA-G7-7502 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-G7-A4TM       TCGA-IA-A40U       TCGA-IA-A40X       TCGA-IA-A40Y 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
      TCGA-J7-8537       TCGA-Q2-A5QZ 
"GPR137 WILD-TYPE" "GPR137 WILD-TYPE" 
                  vv
clus               KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GPR137 MUTATED                    0                                 3
  GPR137 WILD-TYPE                 66                               438
                  vv
clus               KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GPR137 MUTATED                                       1
  GPR137 WILD-TYPE                                   160
D70V9, multiclass
                                       clus
vv                                      GPR137 MUTATED GPR137 WILD-TYPE
  KIDNEY CHROMOPHOBE                                 0               66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  3              438
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              1              160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
D70V11, continuous
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GPR137 MUTATED                                  0     0
  GPR137 WILD-TYPE                                2    11
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  GPR137 MUTATED                           0     4
  GPR137 WILD-TYPE                        65   565
D70V12, multiclass
                                  clus
vv                                 GPR137 MUTATED GPR137 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                2
  ASIAN                                         0               11
  BLACK OR AFRICAN AMERICAN                     0               65
  WHITE                                         4              565
[1] 4 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
  GPR137 MUTATED     0   3
  GPR137 WILD-TYPE  32 438
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GPR137 MUTATED      0    3
  GPR137 WILD-TYPE   32  438
                        clus
vv                       GPR137 MUTATED GPR137 WILD-TYPE
  HISPANIC OR LATINO                  0               32
  NOT HISPANIC OR LATINO              3              438
[1] 2 2
[1] FALSE

Clustering(71) Variable = GFM1 MUTATION ANALYSIS
D71V1, survival
                sevent
clus2              0   1
  GFM1 MUTATED     2   1
  GFM1 WILD-TYPE 484 174
  GFM1 MUTATED GFM1 WILD-TYPE 
             3            658 
  GFM1 MUTATED GFM1 WILD-TYPE 
             1            174 
$`GFM1 MUTATED`
TCGA-KN-8426 TCGA-KO-8406 TCGA-KO-8408 
        3.55        79.04        16.67 

$`GFM1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         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-8407 
       42.35       100.87        76.90        10.68        74.93        92.71 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 
       61.58        63.95        39.16        49.08        49.02        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38        48.82        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       20.28       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       60.92        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 
       52.21        45.07        33.50        16.77         6.02        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       34.36         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       79.36        92.98       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
       74.66         1.35        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 
       54.90        34.19        19.00        24.89        10.68         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       13.68        25.84         6.38       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65         1.05        12.43        17.95        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
        2.04        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       11.97        29.10        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       20.25        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       92.58        12.85        17.75        14.07 

  GFM1 MUTATED GFM1 WILD-TYPE 
          3.55           0.07 
  GFM1 MUTATED GFM1 WILD-TYPE 
         79.04         194.79 
  GFM1 MUTATED GFM1 WILD-TYPE 
        16.670         34.325 
[1] "3.5 - 79.0 (16.7)"  "0.1 - 194.8 (34.3)"
[1] "hr=" "1.5"
D71V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GFM1 MUTATED         1        0         1        1
  GFM1 WILD-TYPE     326       79       164       85
D71V3, multiclass
           clus
vv          GFM1 MUTATED GFM1 WILD-TYPE
  STAGE I              1            326
  STAGE II             0             79
  STAGE III            1            164
  STAGE IV             1             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
  GFM1 MUTATED     1   0   2   0
  GFM1 WILD-TYPE 339  97 219  10
D71V4, multiclass
    clus
vv   GFM1 MUTATED GFM1 WILD-TYPE
  T1            1            339
  T2            0             97
  T3            2            219
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  GFM1 MUTATED     1   1   0
  GFM1 WILD-TYPE 271  35   6
D71V5, multiclass
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             2            312 
    TCGA-KL-8326     TCGA-KL-8327     TCGA-KL-8328     TCGA-KL-8329 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8330     TCGA-KL-8331     TCGA-KL-8332     TCGA-KL-8333 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8334     TCGA-KL-8335     TCGA-KL-8336     TCGA-KL-8337 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8338     TCGA-KL-8339     TCGA-KL-8340     TCGA-KL-8341 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8342     TCGA-KL-8343     TCGA-KL-8344     TCGA-KL-8345 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8346     TCGA-KM-8438     TCGA-KM-8443     TCGA-KN-8418 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8419     TCGA-KN-8421     TCGA-KN-8422     TCGA-KN-8423 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8424     TCGA-KN-8425     TCGA-KN-8427     TCGA-KN-8428 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KN-8429     TCGA-KN-8430     TCGA-KO-8405     TCGA-KO-8407 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8410     TCGA-KO-8413     TCGA-KO-8414 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8415     TCGA-KO-8416     TCGA-KO-8417     TCGA-A3-3317 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A3-3331     TCGA-A3-3347     TCGA-A3-3349     TCGA-A3-3357 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A3-3358     TCGA-A3-3362     TCGA-A3-3363     TCGA-A3-3367 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A3-3370     TCGA-A3-3373     TCGA-A3-3374     TCGA-A3-3376 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A3-3380     TCGA-A3-3385     TCGA-A3-3387     TCGA-AK-3425 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-AK-3427     TCGA-AK-3428     TCGA-AK-3429     TCGA-AK-3430 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-AK-3436     TCGA-AK-3443     TCGA-AK-3450     TCGA-AK-3451 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-AK-3456     TCGA-B0-4690     TCGA-B0-4691     TCGA-B0-4693 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-4703     TCGA-B0-4710     TCGA-B0-4810     TCGA-B0-4811 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-4814     TCGA-B0-4816     TCGA-B0-4817     TCGA-B0-4823 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-4824     TCGA-B0-4827     TCGA-B0-4833     TCGA-B0-4837 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B0-4839     TCGA-B0-4842     TCGA-B0-4843 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-4846     TCGA-B0-4852     TCGA-B0-4945     TCGA-B0-5075 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5077     TCGA-B0-5080     TCGA-B0-5081     TCGA-B0-5083 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5084     TCGA-B0-5085     TCGA-B0-5088     TCGA-B0-5092 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5094     TCGA-B0-5095     TCGA-B0-5096     TCGA-B0-5097 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5104     TCGA-B0-5106     TCGA-B0-5107     TCGA-B0-5108 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5109     TCGA-B0-5110     TCGA-B0-5113     TCGA-B0-5115 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5116     TCGA-B0-5119     TCGA-B0-5120     TCGA-B0-5121 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5399     TCGA-B0-5400     TCGA-B0-5691     TCGA-B0-5692 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5694     TCGA-B0-5695     TCGA-B0-5696     TCGA-B0-5697 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5698     TCGA-B0-5699     TCGA-B0-5701     TCGA-B0-5702 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5703     TCGA-B0-5705     TCGA-B0-5706     TCGA-B0-5707 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B0-5710     TCGA-B0-5712     TCGA-B0-5713     TCGA-B2-5633 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B2-5641     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-B8-4143     TCGA-B8-4148     TCGA-B8-4151 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B8-4154     TCGA-B8-4619     TCGA-B8-4620     TCGA-B8-4621 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B8-4622     TCGA-B8-5158     TCGA-B8-5159     TCGA-B8-5163 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-B8-5165     TCGA-B8-5545     TCGA-B8-5546 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B8-5549     TCGA-B8-5550     TCGA-B8-5551     TCGA-B8-5553 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4158     TCGA-BP-4159     TCGA-BP-4160     TCGA-BP-4162 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4163     TCGA-BP-4165     TCGA-BP-4166     TCGA-BP-4169 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4170     TCGA-BP-4173     TCGA-BP-4174     TCGA-BP-4326 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4329     TCGA-BP-4330     TCGA-BP-4331     TCGA-BP-4337 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4338     TCGA-BP-4340     TCGA-BP-4342     TCGA-BP-4343 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4345     TCGA-BP-4346     TCGA-BP-4351     TCGA-BP-4352 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4354     TCGA-BP-4756     TCGA-BP-4761     TCGA-BP-4768 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4770     TCGA-BP-4771     TCGA-BP-4787     TCGA-BP-4795 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4797     TCGA-BP-4798     TCGA-BP-4799     TCGA-BP-4960 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4964     TCGA-BP-4967     TCGA-BP-4968     TCGA-BP-4970 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4971     TCGA-BP-4974     TCGA-BP-4985     TCGA-BP-4986 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-4988     TCGA-BP-4989     TCGA-BP-4995     TCGA-BP-5006 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-5007     TCGA-BP-5010     TCGA-BP-5169     TCGA-BP-5182 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-5186     TCGA-BP-5191     TCGA-BP-5198     TCGA-BP-5199 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BP-5201     TCGA-CJ-4636     TCGA-CJ-4638     TCGA-CJ-4639 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CJ-4640     TCGA-CJ-4643     TCGA-CJ-4644     TCGA-CJ-4868 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CJ-4869     TCGA-CJ-4872     TCGA-CJ-4873     TCGA-CJ-4874 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CJ-4876     TCGA-CJ-4890     TCGA-CJ-4891     TCGA-CJ-4892 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CJ-4894     TCGA-CJ-4900     TCGA-CJ-4904     TCGA-CJ-4918 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CJ-5678     TCGA-CJ-6030     TCGA-CJ-6033     TCGA-CW-5585 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CW-5591     TCGA-CW-6087     TCGA-CZ-4854     TCGA-CZ-4856 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CZ-4857     TCGA-CZ-4859     TCGA-CZ-4863     TCGA-CZ-5451 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CZ-5452     TCGA-CZ-5454     TCGA-CZ-5456     TCGA-CZ-5467 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CZ-5469     TCGA-CZ-5470     TCGA-CZ-5984     TCGA-CZ-5985 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-CZ-5986     TCGA-CZ-5988     TCGA-CZ-5989     TCGA-A4-7583 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7915     TCGA-A4-A57E     TCGA-A4-A5Y1 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B1-A655     TCGA-B1-A656     TCGA-B1-A657 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7058 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-G7-6795     TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-GL-A59R     TCGA-IA-A40U     TCGA-IA-A40Y     TCGA-J7-6720 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-J7-8537     TCGA-P4-A5E6     TCGA-P4-A5E8     TCGA-P4-A5EA 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
D71V6, binary
                cls
clus               0   1
  GFM1 MUTATED     1   1
  GFM1 WILD-TYPE 467  77
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      1    1
  GFM1 WILD-TYPE  467   77
   clus
vv  GFM1 MUTATED GFM1 WILD-TYPE
  0            1            467
  1            1             77
[1] 2 2
[1] FALSE
D71V7, binary
                cls
clus               0   1
  GFM1 MUTATED     1   2
  GFM1 WILD-TYPE 228 437
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      1    2
  GFM1 WILD-TYPE  228  437
        clus
vv       GFM1 MUTATED GFM1 WILD-TYPE
  FEMALE            1            228
  MALE              2            437
[1] 2 2
[1] FALSE
D71V8, continuous
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  GFM1 MUTATED                    3                                 0
  GFM1 WILD-TYPE                 63                               441
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  GFM1 MUTATED                                       0
  GFM1 WILD-TYPE                                   161
D71V9, multiclass
                                       clus
vv                                      GFM1 MUTATED GFM1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               3             63
  KIDNEY CLEAR CELL RENAL CARCINOMA                0            441
  KIDNEY PAPILLARY RENAL CELL CARCINOMA            0            161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             1             41 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KL-8345     TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KO-8409     TCGA-KO-8416     TCGA-B8-4621     TCGA-B8-5158 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B8-5164     TCGA-A4-8310     TCGA-A4-A48D     TCGA-A4-A57E 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A4-A5Y0     TCGA-AL-3466     TCGA-AL-3472     TCGA-AL-7173 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B1-A654     TCGA-B9-4115     TCGA-B9-4117     TCGA-B9-7268 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-B9-A44B     TCGA-B9-A69E     TCGA-DW-5561     TCGA-DW-7834 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773     TCGA-GL-A59T 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-HE-A5NJ     TCGA-HE-A5NK     TCGA-IA-A40U 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-IZ-A6M8     TCGA-P4-A5E7     TCGA-P4-A5EB     TCGA-PJ-A5Z9 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"GFM1 WILD-TYPE" 
D71V11, continuous
[1] "Remove cluster labels:" "GFM1 MUTATED"          
clus
  GFM1 MUTATED GFM1 WILD-TYPE 
             1             25 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8409     TCGA-B8-5158 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0     TCGA-AL-3472 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117     TCGA-B9-A69E 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" "GFM1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"GFM1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GFM1 MUTATED                                  0     0
  GFM1 WILD-TYPE                                2    11
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GFM1 MUTATED                           0     3
  GFM1 WILD-TYPE                        65   566
D71V12, multiclass
                                  clus
vv                                 GFM1 MUTATED GFM1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       0             11
  BLACK OR AFRICAN AMERICAN                   0             65
  WHITE                                       3            566
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                cls
clus               0   1
  GFM1 MUTATED     0   2
  GFM1 WILD-TYPE  32 439
[1] "tbl2"
                cls
clus             [,1] [,2]
  GFM1 MUTATED      0    2
  GFM1 WILD-TYPE   32  439
                        clus
vv                       GFM1 MUTATED GFM1 WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO            2            439
[1] 2 2
[1] FALSE

Clustering(72) Variable = FAT1 MUTATION ANALYSIS
D72V1, survival
                sevent
clus2              0   1
  FAT1 MUTATED    17   5
  FAT1 WILD-TYPE 469 170
  FAT1 MUTATED FAT1 WILD-TYPE 
            22            639 
  FAT1 MUTATED FAT1 WILD-TYPE 
             5            170 
$`FAT1 MUTATED`
TCGA-KN-8436 TCGA-B0-5098 TCGA-B0-5713 TCGA-B8-4621 TCGA-B8-5550 TCGA-BP-4169 
       42.35        52.08        61.32        25.91        14.27        23.05 
TCGA-BP-4803 TCGA-CJ-4641 TCGA-CZ-4859 TCGA-B1-A657 TCGA-B9-4116 TCGA-B9-7268 
        6.71        54.61        58.75         6.58        20.61        22.06 
TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5885 TCGA-BQ-7061 TCGA-G7-6797 TCGA-GL-A59T 
       14.86         8.88        30.28         7.17        25.15        17.95 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A562 TCGA-P4-A5E8 
       22.26         0.13        20.25        42.94 

$`FAT1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       11.24        11.90        34.36         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       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        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 
       21.30        11.77        10.36        21.57         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.55        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.53        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       89.36        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       36.95        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4861 
       25.45        46.16         0.59        47.08        69.21        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 
       23.90        18.12         3.91         6.77         4.18        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28        23.31        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        19.56        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46        33.83        10.09        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B 
       50.50        28.18        26.40         0.46        43.99         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       19.23         6.81         0.16        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         3.81        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 
       34.19        19.00        24.89        10.68         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        39.25        34.82        13.68        25.84 
TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        6.38       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.43        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 
        5.49        16.80        19.99         2.04        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       12.36        11.97        29.10        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       27.65        99.78        87.22         6.61        84.95        92.58 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       12.85        17.75        14.07 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.13           0.07 
  FAT1 MUTATED FAT1 WILD-TYPE 
         61.32         194.79 
  FAT1 MUTATED FAT1 WILD-TYPE 
         22.16          34.95 
[1] "0.1 - 61.3 (22.2)"  "0.1 - 194.8 (35.0)"
[1] "hr=" "1.3"
D72V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         7        4         8        2
  FAT1 WILD-TYPE     320       75       157       84
D72V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              7            320
  STAGE II             4             75
  STAGE III            8            157
  STAGE IV             2             84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              T1  T2  T3  T4
  FAT1 MUTATED     8   6   8   0
  FAT1 WILD-TYPE 332  91 213  10
D72V4, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  T1            8            332
  T2            6             91
  T3            8            213
  T4            0             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus              N0  N1  N2
  FAT1 MUTATED     8   3   0
  FAT1 WILD-TYPE 264  33   6
D72V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0            8            264
  N1            3             33
  N2            0              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                cls
clus               0   1
  FAT1 MUTATED    13   2
  FAT1 WILD-TYPE 455  76
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED     13    2
  FAT1 WILD-TYPE  455   76
   clus
vv  FAT1 MUTATED FAT1 WILD-TYPE
  0           13            455
  1            2             76
[1] 2 2
[1] FALSE
D72V7, binary
                cls
clus               0   1
  FAT1 MUTATED     8  14
  FAT1 WILD-TYPE 221 425
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      8   14
  FAT1 WILD-TYPE  221  425
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE            8            221
  MALE             14            425
[1] 2 2
[1] FALSE
D72V8, continuous
[1] "Remove cluster labels:" "FAT1 MUTATED"          
clus
  FAT1 MUTATED FAT1 WILD-TYPE 
             2             77 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411     TCGA-KO-8413     TCGA-AK-3430 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B0-4838     TCGA-B4-5377     TCGA-B4-5832     TCGA-B4-5834 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B4-5835     TCGA-B4-5836     TCGA-B4-5838     TCGA-B4-5843 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B4-5844     TCGA-CZ-4854     TCGA-CZ-4856     TCGA-CZ-4858 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456     TCGA-CZ-5457 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982     TCGA-DV-5565 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569     TCGA-DV-5574 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904     TCGA-EU-5905 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-EU-5907     TCGA-A4-7286     TCGA-A4-7828     TCGA-A4-8310 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-8311     TCGA-A4-8312     TCGA-A4-8518     TCGA-A4-8630 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-A4ZT     TCGA-A4-A57E     TCGA-A4-A5DU     TCGA-A4-A5XZ 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-A4-A6HP     TCGA-AL-3466     TCGA-DW-5560     TCGA-DW-5561 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-DW-7963 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6796     TCGA-G7-7501     TCGA-G7-7502 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-G7-A4TM     TCGA-IA-A40U     TCGA-IA-A40X     TCGA-IA-A40Y 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"FAT1 WILD-TYPE" 
                vv
clus             KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  FAT1 MUTATED                    1                                 8
  FAT1 WILD-TYPE                 65                               433
                vv
clus             KIDNEY PAPILLARY RENAL CELL CARCINOMA
  FAT1 MUTATED                                      13
  FAT1 WILD-TYPE                                   148
D72V9, multiclass
                                       clus
vv                                      FAT1 MUTATED FAT1 WILD-TYPE
  KIDNEY CHROMOPHOBE                               1             65
  KIDNEY CLEAR CELL RENAL CARCINOMA                8            433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA           13            148
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
D72V11, continuous
[1] "Remove cluster labels:" "FAT1 MUTATED"          
clus
  FAT1 MUTATED FAT1 WILD-TYPE 
             1             25 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KL-8345 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8433     TCGA-KO-8408     TCGA-KO-8409 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-B8-5158     TCGA-A4-A48D     TCGA-A4-A57E     TCGA-A4-A5Y0 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-7173     TCGA-B1-A654     TCGA-B9-4117 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7963     TCGA-G7-7501     TCGA-GL-7773 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-HE-A5NI     TCGA-IA-A40U     TCGA-P4-A5E6     TCGA-PJ-A5Z9 
"FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" "FAT1 WILD-TYPE" 
    TCGA-Q2-A5QZ 
"FAT1 WILD-TYPE" 
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  FAT1 MUTATED                                  0     1
  FAT1 WILD-TYPE                                2    10
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED                           5    16
  FAT1 WILD-TYPE                        60   553
D72V12, multiclass
                                  clus
vv                                 FAT1 MUTATED FAT1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              2
  ASIAN                                       1             10
  BLACK OR AFRICAN AMERICAN                   5             60
  WHITE                                      16            553
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                cls
clus               0   1
  FAT1 MUTATED     0  18
  FAT1 WILD-TYPE  32 423
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      0   18
  FAT1 WILD-TYPE   32  423
                        clus
vv                       FAT1 MUTATED FAT1 WILD-TYPE
  HISPANIC OR LATINO                0             32
  NOT HISPANIC OR LATINO           18            423
[1] 2 2
[1] FALSE

Clustering(73) Variable = RRP12 MUTATION ANALYSIS
D73V1, survival
                 sevent
clus2               0   1
  RRP12 MUTATED     7   2
  RRP12 WILD-TYPE 479 173
  RRP12 MUTATED RRP12 WILD-TYPE 
              9             652 
  RRP12 MUTATED RRP12 WILD-TYPE 
              2             173 
$`RRP12 MUTATED`
TCGA-KL-8324 TCGA-B0-5080 TCGA-B4-5835 TCGA-BP-4347 TCGA-BP-4972 TCGA-CJ-4889 
      141.73        11.24         0.53        44.94        49.38        63.98 
TCGA-DZ-6133 TCGA-MH-A55Z TCGA-PJ-A5Z9 
       51.19        27.78        17.75 

$`RRP12 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-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        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3311 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3347 
       49.02        48.59        36.36        37.38        48.82        52.93 
TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        88.37        42.97        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 
       74.63        74.76        53.29        43.20        55.76        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 
       28.31        65.52        20.28       109.91        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       66.31        15.78        60.92        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.90        34.36         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
      120.59        79.36        92.98       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        0.23         1.25         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.53        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        64.27        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.84        49.08        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4974 
        6.74        57.40        14.24        48.89        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 
       69.86        64.18        30.64        51.52        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       62.10        73.35        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       69.21        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        6.77         4.18        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       29.46        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       24.56         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       10.09        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       26.40        20.61         0.46        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 
       19.23         6.81         0.16        14.86        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.81        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       10.68         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-6846 
       34.82        25.15        13.68        25.84         6.38       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80        19.99         2.04        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A560 
       12.36         0.13        11.97        29.10        34.29        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       27.65        20.25        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       84.95        92.58        12.85        14.07 

  RRP12 MUTATED RRP12 WILD-TYPE 
           0.53            0.07 
  RRP12 MUTATED RRP12 WILD-TYPE 
         141.73          194.79 
  RRP12 MUTATED RRP12 WILD-TYPE 
          44.94           34.24 
[1] "0.5 - 141.7 (44.9)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.2"
D73V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RRP12 MUTATED         5        1         2        1
  RRP12 WILD-TYPE     322       78       163       85
D73V3, multiclass
           clus
vv          RRP12 MUTATED RRP12 WILD-TYPE
  STAGE I               5             322
  STAGE II              1              78
  STAGE III             2             163
  STAGE IV              1              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
  RRP12 MUTATED     5   1   3   0
  RRP12 WILD-TYPE 335  96 218  10
D73V4, multiclass
    clus
vv   RRP12 MUTATED RRP12 WILD-TYPE
  T1             5             335
  T2             1              96
  T3             3             218
  T4             0              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus               N0  N1  N2
  RRP12 MUTATED     2   0   0
  RRP12 WILD-TYPE 270  36   6
D73V5, multiclass
[1] "Remove cluster labels:" "RRP12 MUTATED"         
clus
  RRP12 MUTATED RRP12 WILD-TYPE 
              2             312 
     TCGA-KL-8326      TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KL-8330      TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KL-8334      TCGA-KL-8335      TCGA-KL-8336      TCGA-KL-8337 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KL-8338      TCGA-KL-8339      TCGA-KL-8340      TCGA-KL-8341 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KL-8342      TCGA-KL-8343      TCGA-KL-8344      TCGA-KL-8345 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KL-8346      TCGA-KM-8438      TCGA-KM-8443      TCGA-KN-8418 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KN-8419      TCGA-KN-8421      TCGA-KN-8422      TCGA-KN-8423 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KN-8424      TCGA-KN-8425      TCGA-KN-8427      TCGA-KN-8428 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KN-8429      TCGA-KN-8430      TCGA-KO-8405      TCGA-KO-8406 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KO-8407      TCGA-KO-8408      TCGA-KO-8409      TCGA-KO-8410 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KO-8413      TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KO-8417      TCGA-A3-3317      TCGA-A3-3331      TCGA-A3-3347 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A3-3349      TCGA-A3-3357      TCGA-A3-3358      TCGA-A3-3362 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A3-3363      TCGA-A3-3367      TCGA-A3-3370      TCGA-A3-3373 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A3-3374      TCGA-A3-3376      TCGA-A3-3380      TCGA-A3-3385 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A3-3387      TCGA-AK-3425      TCGA-AK-3427      TCGA-AK-3428 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-AK-3429      TCGA-AK-3430      TCGA-AK-3436      TCGA-AK-3443 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-AK-3450      TCGA-AK-3451      TCGA-AK-3456      TCGA-B0-4690 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4691      TCGA-B0-4693      TCGA-B0-4703      TCGA-B0-4710 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4810      TCGA-B0-4811      TCGA-B0-4814      TCGA-B0-4816 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4817      TCGA-B0-4823      TCGA-B0-4824      TCGA-B0-4827 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4833      TCGA-B0-4837      TCGA-B0-4838      TCGA-B0-4839 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4842      TCGA-B0-4843      TCGA-B0-4846      TCGA-B0-4852 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4945      TCGA-B0-5075      TCGA-B0-5077      TCGA-B0-5081 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5083      TCGA-B0-5084      TCGA-B0-5085      TCGA-B0-5088 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5092      TCGA-B0-5094      TCGA-B0-5095      TCGA-B0-5096 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5097      TCGA-B0-5104      TCGA-B0-5106      TCGA-B0-5107 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5108      TCGA-B0-5109      TCGA-B0-5110      TCGA-B0-5113 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5115      TCGA-B0-5116      TCGA-B0-5119      TCGA-B0-5120 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5121      TCGA-B0-5399      TCGA-B0-5400      TCGA-B0-5691 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5692      TCGA-B0-5694      TCGA-B0-5695      TCGA-B0-5696 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5697      TCGA-B0-5698      TCGA-B0-5699      TCGA-B0-5701 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5702      TCGA-B0-5703      TCGA-B0-5705      TCGA-B0-5706 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-5707      TCGA-B0-5710      TCGA-B0-5712      TCGA-B0-5713 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B2-5633      TCGA-B2-5641      TCGA-B4-5377      TCGA-B4-5832 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B4-5834      TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B4-5844      TCGA-B8-4143      TCGA-B8-4148      TCGA-B8-4151 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-4154      TCGA-B8-4619      TCGA-B8-4620      TCGA-B8-4621 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-4622      TCGA-B8-5158      TCGA-B8-5159      TCGA-B8-5163 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-5164      TCGA-B8-5165      TCGA-B8-5545      TCGA-B8-5546 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-5549      TCGA-B8-5550      TCGA-B8-5551      TCGA-B8-5553 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4158      TCGA-BP-4159      TCGA-BP-4160      TCGA-BP-4162 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4163      TCGA-BP-4165      TCGA-BP-4166      TCGA-BP-4169 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4170      TCGA-BP-4173      TCGA-BP-4174      TCGA-BP-4326 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4329      TCGA-BP-4330      TCGA-BP-4331      TCGA-BP-4337 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4338      TCGA-BP-4340      TCGA-BP-4342      TCGA-BP-4343 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4345      TCGA-BP-4346      TCGA-BP-4351      TCGA-BP-4352 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4354      TCGA-BP-4756      TCGA-BP-4761      TCGA-BP-4768 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4770      TCGA-BP-4771      TCGA-BP-4787      TCGA-BP-4795 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4797      TCGA-BP-4798      TCGA-BP-4799      TCGA-BP-4960 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4964      TCGA-BP-4967      TCGA-BP-4968      TCGA-BP-4970 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4971      TCGA-BP-4974      TCGA-BP-4985      TCGA-BP-4986 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-4988      TCGA-BP-4989      TCGA-BP-4995      TCGA-BP-5006 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-5007      TCGA-BP-5010      TCGA-BP-5169      TCGA-BP-5182 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-5186      TCGA-BP-5191      TCGA-BP-5198      TCGA-BP-5199 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BP-5201      TCGA-CJ-4636      TCGA-CJ-4638      TCGA-CJ-4639 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CJ-4640      TCGA-CJ-4643      TCGA-CJ-4644      TCGA-CJ-4868 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CJ-4869      TCGA-CJ-4872      TCGA-CJ-4873      TCGA-CJ-4874 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CJ-4876      TCGA-CJ-4890      TCGA-CJ-4891      TCGA-CJ-4892 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CJ-4894      TCGA-CJ-4900      TCGA-CJ-4904      TCGA-CJ-4918 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CJ-5678      TCGA-CJ-6030      TCGA-CJ-6033      TCGA-CW-5585 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CW-5591      TCGA-CW-6087      TCGA-CZ-4854      TCGA-CZ-4856 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-4857      TCGA-CZ-4859      TCGA-CZ-4863      TCGA-CZ-5451 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-5452      TCGA-CZ-5454      TCGA-CZ-5456      TCGA-CZ-5467 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5470      TCGA-CZ-5984      TCGA-CZ-5985 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-5986      TCGA-CZ-5988      TCGA-CZ-5989      TCGA-A4-7583 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7915      TCGA-A4-A57E      TCGA-A4-A5Y1 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B1-A655      TCGA-B1-A656      TCGA-B1-A657 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885      TCGA-BQ-5887 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7045 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7058 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DW-7963      TCGA-DZ-6131      TCGA-G7-6789      TCGA-G7-6793 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-G7-6795      TCGA-G7-7501      TCGA-GL-6846      TCGA-GL-7966 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-GL-A59R      TCGA-IA-A40U      TCGA-IA-A40Y      TCGA-J7-6720 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-J7-8537      TCGA-P4-A5E6      TCGA-P4-A5E8      TCGA-P4-A5EA 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
D73V6, binary
                 cls
clus                0   1
  RRP12 MUTATED     5   1
  RRP12 WILD-TYPE 463  77
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP12 MUTATED      5    1
  RRP12 WILD-TYPE  463   77
   clus
vv  RRP12 MUTATED RRP12 WILD-TYPE
  0             5             463
  1             1              77
[1] 2 2
[1] FALSE
D73V7, binary
                 cls
clus                0   1
  RRP12 MUTATED     6   3
  RRP12 WILD-TYPE 223 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP12 MUTATED      6    3
  RRP12 WILD-TYPE  223  436
        clus
vv       RRP12 MUTATED RRP12 WILD-TYPE
  FEMALE             6             223
  MALE               3             436
[1] 2 2
[1] FALSE
D73V8, continuous
[1] "Remove cluster labels:" "RRP12 MUTATED"         
clus
  RRP12 MUTATED RRP12 WILD-TYPE 
              1              78 
     TCGA-KM-8438      TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KM-8442      TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KO-8411      TCGA-KO-8413      TCGA-AK-3430 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-B4-5832      TCGA-B4-5834 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B4-5836      TCGA-B4-5838      TCGA-B4-5843      TCGA-B4-5844 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-4854      TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-4862      TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5465 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-CZ-5469      TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DV-5568      TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DV-5576      TCGA-EU-5904      TCGA-EU-5905      TCGA-EU-5907 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-A4-8310      TCGA-A4-8311 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A4-8312      TCGA-A4-8518      TCGA-A4-8630      TCGA-A4-A4ZT 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A4-A57E      TCGA-A4-A5DU      TCGA-A4-A5XZ      TCGA-A4-A6HP 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-AL-3466      TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DW-7841      TCGA-DW-7842      TCGA-DW-7963      TCGA-EV-5901 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-G7-A4TM      TCGA-IA-A40U      TCGA-IA-A40X      TCGA-IA-A40Y 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-J7-8537      TCGA-Q2-A5QZ 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
                 vv
clus              KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  RRP12 MUTATED                    1                                 5
  RRP12 WILD-TYPE                 65                               436
                 vv
clus              KIDNEY PAPILLARY RENAL CELL CARCINOMA
  RRP12 MUTATED                                       3
  RRP12 WILD-TYPE                                   158
D73V9, multiclass
                                       clus
vv                                      RRP12 MUTATED RRP12 WILD-TYPE
  KIDNEY CHROMOPHOBE                                1              65
  KIDNEY CLEAR CELL RENAL CARCINOMA                 5             436
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             3             158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
[1] "Remove cluster labels:" "RRP12 MUTATED"         
clus
  RRP12 MUTATED RRP12 WILD-TYPE 
              2              40 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8428      TCGA-KN-8433      TCGA-KO-8408 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8416      TCGA-B8-4621      TCGA-B8-5158 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-5164      TCGA-A4-8310      TCGA-A4-A48D      TCGA-A4-A57E 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-A4-A5Y0      TCGA-AL-3466      TCGA-AL-3472      TCGA-AL-7173 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B1-A654      TCGA-B9-4115      TCGA-B9-4117      TCGA-B9-7268 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B9-A44B      TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7834 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-DW-7963      TCGA-G7-7501      TCGA-GL-7773      TCGA-GL-A59T 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-HE-A5NI      TCGA-HE-A5NJ      TCGA-HE-A5NK      TCGA-IA-A40U 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-IZ-A6M8      TCGA-P4-A5E7      TCGA-P4-A5EB      TCGA-Q2-A5QZ 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
D73V11, continuous
[1] "Remove cluster labels:" "RRP12 MUTATED"         
clus
  RRP12 MUTATED RRP12 WILD-TYPE 
              1              25 
     TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341      TCGA-KL-8345 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408      TCGA-KO-8409 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B8-5158      TCGA-A4-A48D      TCGA-A4-A57E      TCGA-A4-A5Y0 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-7173      TCGA-B1-A654      TCGA-B9-4117 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-B9-A69E      TCGA-DW-5561      TCGA-DW-7963      TCGA-G7-7501 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-GL-7773      TCGA-HE-A5NI      TCGA-IA-A40U      TCGA-P4-A5E6 
"RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" "RRP12 WILD-TYPE" 
     TCGA-Q2-A5QZ 
"RRP12 WILD-TYPE" 
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RRP12 MUTATED                                  0     0
  RRP12 WILD-TYPE                                2    11
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  RRP12 MUTATED                           1     8
  RRP12 WILD-TYPE                        64   561
D73V12, multiclass
                                  clus
vv                                 RRP12 MUTATED RRP12 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               2
  ASIAN                                        0              11
  BLACK OR AFRICAN AMERICAN                    1              64
  WHITE                                        8             561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                 cls
clus                0   1
  RRP12 MUTATED     1   5
  RRP12 WILD-TYPE  31 436
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RRP12 MUTATED      1    5
  RRP12 WILD-TYPE   31  436
                        clus
vv                       RRP12 MUTATED RRP12 WILD-TYPE
  HISPANIC OR LATINO                 1              31
  NOT HISPANIC OR LATINO             5             436
[1] 2 2
[1] FALSE
