[1] "ofn"        "-oTPRAD-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/PRAD-TP/15087329/PRAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/15170475/transformed.cor.cli.txt"

nPatients in clinical file=489, in cluster file=425, common to both=420
[1] "Reduce the number of clustering variables from 64 to 62."
[1]  62 420
[1] "SPOP MUTATION ANALYSIS"
[1] 3
  SPOP MUTATED SPOP WILD-TYPE 
            48            372 
  SPOP MUTATED SPOP WILD-TYPE 
            48            372 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            42            378 
  TP53 MUTATED TP53 WILD-TYPE 
            42            378 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            14            406 
  PTEN MUTATED PTEN WILD-TYPE 
            14            406 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              11              409 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              11              409 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             25             395 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             25             395 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           19           401 
  ATM MUTATED ATM WILD-TYPE 
           19           401 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              11              409 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              11              409 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
             8            412 
  BRAF MUTATED BRAF WILD-TYPE 
             8            412 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             5            415 
  HRAS MUTATED HRAS WILD-TYPE 
             5            415 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
              9             411 
  KDM6A MUTATED KDM6A WILD-TYPE 
              9             411 
[1] "IDH1 MUTATION ANALYSIS"
[1] 3
  IDH1 MUTATED IDH1 WILD-TYPE 
             5            415 
  IDH1 MUTATED IDH1 WILD-TYPE 
             5            415 
[1] "SMG7 MUTATION ANALYSIS"
[1] 3
  SMG7 MUTATED SMG7 WILD-TYPE 
             7            413 
  SMG7 MUTATED SMG7 WILD-TYPE 
             7            413 
[1] "ZMYM3 MUTATION ANALYSIS"
[1] 3
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              9             411 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              9             411 
[1] "EHHADH MUTATION ANALYSIS"
[1] 3
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              415 
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              415 
[1] "TP53BP1 MUTATION ANALYSIS"
[1] 3
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                7               413 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                7               413 
[1] "CNTNAP1 MUTATION ANALYSIS"
[1] 3
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                7               413 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                7               413 
[1] "BMP2K MUTATION ANALYSIS"
[1] 3
  BMP2K MUTATED BMP2K WILD-TYPE 
              6             414 
  BMP2K MUTATED BMP2K WILD-TYPE 
              6             414 
[1] "RPTN MUTATION ANALYSIS"
[1] 3
  RPTN MUTATED RPTN WILD-TYPE 
             6            414 
  RPTN MUTATED RPTN WILD-TYPE 
             6            414 
[1] "TCEB3 MUTATION ANALYSIS"
[1] 3
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             416 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             416 
[1] "NTM MUTATION ANALYSIS"
[1] 3
  NTM MUTATED NTM WILD-TYPE 
            5           415 
  NTM MUTATED NTM WILD-TYPE 
            5           415 
[1] "MED12 MUTATION ANALYSIS"
[1] 3
  MED12 MUTATED MED12 WILD-TYPE 
              7             413 
  MED12 MUTATED MED12 WILD-TYPE 
              7             413 
[1] "MED15 MUTATION ANALYSIS"
[1] 3
  MED15 MUTATED MED15 WILD-TYPE 
              6             414 
  MED15 MUTATED MED15 WILD-TYPE 
              6             414 
[1] "ERN1 MUTATION ANALYSIS"
[1] 3
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            417 
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            417 
[1] "LMOD2 MUTATION ANALYSIS"
[1] 3
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              5             415 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              5             415 
[1] "FAM111A MUTATION ANALYSIS"
[1] 3
  FAM111A MUTATED FAM111A WILD-TYPE 
                3               417 
  FAM111A MUTATED FAM111A WILD-TYPE 
                3               417 
[1] "ZNF709 MUTATION ANALYSIS"
[1] 3
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              415 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              415 
[1] "MLLT10 MUTATION ANALYSIS"
[1] 3
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              416 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              416 
[1] "TNRC18 MUTATION ANALYSIS"
[1] 3
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              416 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              416 
[1] "GAGE2D MUTATION ANALYSIS"
[1] 3
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               3              417 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               3              417 
[1] "EMG1 MUTATION ANALYSIS"
[1] 3
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            416 
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            416 
[1] "LAMA3 MUTATION ANALYSIS"
[1] 3
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              7             413 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              7             413 
[1] "RPL11 MUTATION ANALYSIS"
[1] 3
  RPL11 MUTATED RPL11 WILD-TYPE 
              4             416 
  RPL11 MUTATED RPL11 WILD-TYPE 
              4             416 
[1] "ZFHX3 MUTATION ANALYSIS"
[1] 3
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             13             407 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             13             407 
[1] "MUC17 MUTATION ANALYSIS"
[1] 3
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             397 
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             397 
[1] "CDKN1B MUTATION ANALYSIS"
[1] 3
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               5              415 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               5              415 
[1] "POM121 MUTATION ANALYSIS"
[1] 3
  POM121 MUTATED POM121 WILD-TYPE 
               3              417 
  POM121 MUTATED POM121 WILD-TYPE 
               3              417 
[1] "ESCO1 MUTATION ANALYSIS"
[1] 3
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             416 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             416 
[1] "MYOT MUTATION ANALYSIS"
[1] 3
  MYOT MUTATED MYOT WILD-TYPE 
             4            416 
  MYOT MUTATED MYOT WILD-TYPE 
             4            416 
[1] "L1CAM MUTATION ANALYSIS"
[1] 3
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             414 
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             414 
[1] "FAM47C MUTATION ANALYSIS"
[1] 3
  FAM47C MUTATED FAM47C WILD-TYPE 
               9              411 
  FAM47C MUTATED FAM47C WILD-TYPE 
               9              411 
[1] "CR1L MUTATION ANALYSIS"
[1] 3
  CR1L MUTATED CR1L WILD-TYPE 
             5            415 
  CR1L MUTATED CR1L WILD-TYPE 
             5            415 
[1] "FAM120B MUTATION ANALYSIS"
[1] 3
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               417 
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               417 
[1] "EDC4 MUTATION ANALYSIS"
[1] 3
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            417 
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            417 
[1] "KIRREL MUTATION ANALYSIS"
[1] 3
  KIRREL MUTATED KIRREL WILD-TYPE 
               5              415 
  KIRREL MUTATED KIRREL WILD-TYPE 
               5              415 
[1] "TCERG1 MUTATION ANALYSIS"
[1] 3
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               4              416 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               4              416 
[1] "SLC16A6 MUTATION ANALYSIS"
[1] 3
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                4               416 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                4               416 
[1] "NKX3-1 MUTATION ANALYSIS"
[1] 3
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              415 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              415 
[1] "RNF17 MUTATION ANALYSIS"
[1] 3
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             417 
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             417 
[1] "KYNU MUTATION ANALYSIS"
[1] 3
  KYNU MUTATED KYNU WILD-TYPE 
             3            417 
  KYNU MUTATED KYNU WILD-TYPE 
             3            417 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             416 
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             416 
[1] "CDK12 MUTATION ANALYSIS"
[1] 3
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             412 
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             412 
[1] "ACPT MUTATION ANALYSIS"
[1] 3
  ACPT MUTATED ACPT WILD-TYPE 
             3            417 
  ACPT MUTATED ACPT WILD-TYPE 
             3            417 
[1] "AP4B1 MUTATION ANALYSIS"
[1] 3
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              5             415 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              5             415 
[1] "RAG1 MUTATION ANALYSIS"
[1] 3
  RAG1 MUTATED RAG1 WILD-TYPE 
             9            411 
  RAG1 MUTATED RAG1 WILD-TYPE 
             9            411 
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
            8           412 
  APC MUTATED APC WILD-TYPE 
            8           412 
[1] "MSLNL MUTATION ANALYSIS"
[1] 3
  MSLNL MUTATED MSLNL WILD-TYPE 
              4             416 
  MSLNL MUTATED MSLNL WILD-TYPE 
              4             416 
[1] "GAB2 MUTATION ANALYSIS"
[1] 3
  GAB2 MUTATED GAB2 WILD-TYPE 
             5            415 
  GAB2 MUTATED GAB2 WILD-TYPE 
             5            415 
[1] "DNMT3B MUTATION ANALYSIS"
[1] 3
  DNMT3B MUTATED DNMT3B WILD-TYPE 
               4              416 
  DNMT3B MUTATED DNMT3B WILD-TYPE 
               4              416 
[1] "NCKAP1L MUTATION ANALYSIS"
[1] 3
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                5               415 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                5               415 
[1] "PRTFDC1 MUTATION ANALYSIS"
[1] 3
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                3               417 
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                3               417 
[1] "PCSK5 MUTATION ANALYSIS"
[1] 3
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              6             414 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              6             414 
[1] "ITGA2B MUTATION ANALYSIS"
[1] 3
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               4              416 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               4              416 
[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] "RADIATION_THERAPY"                     
[14] "HISTOLOGICAL_TYPE"                     
[15] "RADIATIONS_RADIATION_REGIMENINDICATION"
[16] "COMPLETENESS_OF_RESECTION"             
[17] "NUMBER_OF_LYMPH_NODES"                 
[18] "GLEASON_SCORE_COMBINED"                
[19] "GLEASON_SCORE_PRIMARY"                 
[20] "GLEASON_SCORE_SECONDARY"               
[21] "HIGHEST_GLEASON_SCORE"                 
[22] "GLEASON_SCORE"                         
[23] "PSA_RESULT_PREOP"                      
[24] "DAYS_TO_PREOP_PSA"                     
[25] "PSA_VALUE"                             
[26] "DAYS_TO_PSA"                           
[27] "RACE"                                  
[28] "ETHNICITY"                             
[29] "BATCH_NUMBER"                          

Input Data has 29 rows and 420 columns.

[1] "Batch" "29"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=7,	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=374,	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=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'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 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'GLEASON_SCORE_COMBINED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'GLEASON_SCORE_PRIMARY':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'GLEASON_SCORE_SECONDARY':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 21:'HIGHEST_GLEASON_SCORE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HIGHEST_GLEASON_SCORE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 22:'GLEASON_SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 23:'PSA_RESULT_PREOP':	nDistinctValues=189,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 24:'DAYS_TO_PREOP_PSA':	nDistinctValues=196,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 25:'PSA_VALUE':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 26:'DAYS_TO_PSA':	nDistinctValues=327,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 27:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 28:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 29:'BATCH_NUMBER':	nDistinctValues=20,	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] "****** SUMMARY ***** "
Output Data has 420 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"            "PATHOLOGY_T_STAGE"        
 [3] "PATHOLOGY_N_STAGE"         "HISTOLOGICAL_TYPE"        
 [5] "COMPLETENESS_OF_RESECTION" "NUMBER_OF_LYMPH_NODES"    
 [7] "GLEASON_SCORE_COMBINED"    "GLEASON_SCORE_PRIMARY"    
 [9] "GLEASON_SCORE_SECONDARY"   "GLEASON_SCORE"            
[11] "PSA_RESULT_PREOP"          "PSA_VALUE"                
[13] "RACE"                     
YEARS_TO_BIRTH, nv=35, binary=FALSE, numeric=TRUE
PATHOLOGY_T_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T2  T3  T4 
172 239   6 
[1] "table(vv)"
vv
 T2  T3  T4 
172 239   6 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T2  T3  T4 
172 239   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 T2  T3  T4 
172 239   6 
PATHOLOGY_N_STAGE, nv=2, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=10, binary=FALSE, numeric=TRUE
GLEASON_SCORE_COMBINED, nv=6, binary=FALSE, numeric=TRUE
GLEASON_SCORE_PRIMARY, nv=5, binary=FALSE, numeric=TRUE
GLEASON_SCORE_SECONDARY, nv=4, binary=FALSE, numeric=TRUE
GLEASON_SCORE, nv=5, binary=FALSE, numeric=TRUE
PSA_RESULT_PREOP, nv=189, binary=FALSE, numeric=TRUE
PSA_VALUE, nv=87, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SPOP MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  SPOP MUTATED    47   1
  SPOP WILD-TYPE 365   6
  SPOP MUTATED SPOP WILD-TYPE 
            48            371 
  SPOP MUTATED SPOP WILD-TYPE 
             1              6 
$`SPOP MUTATED`
TCGA-CH-5788 TCGA-EJ-5505 TCGA-EJ-5509 TCGA-EJ-5531 TCGA-EJ-7115 TCGA-EJ-7123 
       26.99        30.31        48.13        41.85        88.34        74.10 
TCGA-EJ-7330 TCGA-EJ-7782 TCGA-EJ-8468 TCGA-EJ-A65E TCGA-EJ-A65M TCGA-EJ-A8FS 
        6.28        38.37        77.16        13.71         7.56         8.75 
TCGA-FC-7961 TCGA-G9-6333 TCGA-G9-6338 TCGA-G9-6369 TCGA-G9-7510 TCGA-HC-7080 
       15.42        81.04        66.67        39.95        38.96        36.36 
TCGA-HC-8258 TCGA-HC-8261 TCGA-HC-A6AP TCGA-J4-A6G3 TCGA-J4-A83J TCGA-J9-A52D 
        2.17        17.95         2.33        27.91        22.88         6.97 
TCGA-KC-A7F5 TCGA-KK-A59X TCGA-KK-A59Z TCGA-KK-A6E0 TCGA-KK-A7AQ TCGA-KK-A7B0 
        2.99        56.28        86.40        30.02        52.93        32.84 
TCGA-KK-A8I9 TCGA-KK-A8IF TCGA-KK-A8IK TCGA-QU-A6IM TCGA-VN-A88O TCGA-VN-A88R 
       32.91        26.43        51.39        41.00        15.81        25.78 
TCGA-VP-A878 TCGA-VP-A87B TCGA-VP-A87H TCGA-X4-A8KS TCGA-XJ-A83G TCGA-Y6-A8TL 
       97.41        85.18        21.80        32.19        38.04        25.48 
TCGA-YL-A8HM TCGA-YL-A8S8 TCGA-YL-A8SH TCGA-YL-A8SO TCGA-ZG-A8QX TCGA-ZG-A8QY 
       48.72        62.14        28.77       114.38        14.53        13.28 

$`SPOP WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        15.98         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        23.90        38.93        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       60.23        47.87        29.06        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 
       30.35        27.68        24.39        23.90        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
        3.75        23.05        19.92        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        23.34        12.92        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
       14.83        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        9.83         4.54        28.41        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6336 TCGA-G9-6339 
       16.24         1.78        41.62        87.35        67.99        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
       44.81         3.32        40.18        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       56.75        64.18        50.73        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       28.18        32.68         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       65.26         2.93        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 
       22.42        28.27        23.87         2.27        22.55        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6M7 
       32.05        29.92        27.39         6.02        25.28        16.83 
TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.52        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        5.85        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57       113.10        44.68 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
       77.72       115.86        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU 
       49.25       113.33        67.07        58.19         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B1 TCGA-KK-A7B2 
       27.02        34.65        51.68        49.94        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IG 
       31.79        63.48         2.73        67.43        69.27        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18       113.98        51.25        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         3.19       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88P 
        8.84        25.51        24.53         6.21        15.52        41.42 
TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A879 TCGA-VP-A87C 
       44.91       111.39        75.91       109.58        23.93        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       60.92        66.97        53.36        42.94        14.76        45.47 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
        3.91        37.05        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HO 
       31.99         4.87        52.96        49.02        51.45        71.77 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ 
       60.56        16.83        56.52        41.46        45.14        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29        32.45        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QZ 
       53.36        60.99        62.37         3.09        10.13 

  SPOP MUTATED SPOP WILD-TYPE 
          2.17           0.72 
  SPOP MUTATED SPOP WILD-TYPE 
        114.38         165.17 
  SPOP MUTATED SPOP WILD-TYPE 
        32.515         26.660 
[1] "2.2 - 114.4 (32.5)" "0.7 - 165.2 (26.7)"
[1] "hr=" "1.2"
D1V2, continuous
                vv
clus              T2  T3  T4
  SPOP MUTATED    23  25   0
  SPOP WILD-TYPE 149 214   6
D1V3, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  T2           23            149
  T3           25            214
  T4            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"
D1V4, binary
                cls
clus               0   1
  SPOP MUTATED    39   4
  SPOP WILD-TYPE 260  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED     39    4
  SPOP WILD-TYPE  260   54
   clus
vv  SPOP MUTATED SPOP WILD-TYPE
  0           39            260
  1            4             54
[1] 2 2
[1] FALSE
D1V5, binary
                cls
clus               0   1
  SPOP MUTATED     2  46
  SPOP WILD-TYPE  13 359
[1] "tbl2"
                cls
clus             [,1] [,2]
  SPOP MUTATED      2   46
  SPOP WILD-TYPE   13  359
                                        clus
vv                                       SPOP MUTATED SPOP WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            2             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE              46            359
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SPOP MUTATED    31   8   1   4
  SPOP WILD-TYPE 252  95   4  11
D1V6, multiclass
    clus
vv   SPOP MUTATED SPOP WILD-TYPE
  R0           31            252
  R1            8             95
  R2            1              4
  RX            4             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, continuous
D1V8, continuous
D1V9, continuous
D1V10, continuous
D1V11, continuous
D1V12, continuous
D1V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SPOP MUTATED       0                         1    12
  SPOP WILD-TYPE     2                         6   135
D1V14, multiclass
                           clus
vv                          SPOP MUTATED SPOP WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                               12            135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  TP53 MUTATED    40   2
  TP53 WILD-TYPE 372   5
  TP53 MUTATED TP53 WILD-TYPE 
            42            377 
  TP53 MUTATED TP53 WILD-TYPE 
             2              5 
$`TP53 MUTATED`
TCGA-2A-A8VT TCGA-CH-5761 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5521 TCGA-EJ-5525 
       32.71         0.92        23.90        36.23        51.88        36.66 
TCGA-EJ-7315 TCGA-EJ-7781 TCGA-EJ-8472 TCGA-EJ-A7NH TCGA-G9-6499 TCGA-G9-7510 
       33.14        23.90        24.85        15.58        50.73        38.96 
TCGA-G9-7521 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-8216 TCGA-HC-A48F 
       30.97        40.08         1.68         1.48        22.42        22.36 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HI-7171 TCGA-J4-A67L TCGA-J9-A52B TCGA-KC-A4BL 
        1.78         2.01        43.69        25.32        13.87        30.71 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KK-A6DY TCGA-KK-A7AU TCGA-KK-A7B4 TCGA-KK-A8IG 
        8.65        19.66       115.86        58.36        20.94        82.36 
TCGA-KK-A8II TCGA-V1-A8MJ TCGA-VP-A872 TCGA-VP-A876 TCGA-VP-A87D TCGA-XJ-A9DI 
      113.98        40.44       111.39       109.58        60.92        48.03 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8SB TCGA-YL-A8SJ TCGA-YL-A9WH TCGA-YL-A9WK 
       49.02        51.45        56.52        45.86        14.04        62.37 

$`TP53 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        22.06        33.96         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       31.00         1.02         2.04        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5522 
       60.23        46.55        47.80        52.27        64.50        68.35 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       43.07        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       37.81        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       14.20         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        9.27         9.83         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       56.75        64.18        27.91        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       31.43        19.36        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A4ZV TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        0.76         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-J4-8198 
       25.48        18.84        78.61        88.24        82.92        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       12.30        33.01        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       12.69        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
        2.99         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40        77.72        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       52.93        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       34.95        36.13        29.56        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       69.27        26.43        66.18        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        29.23        18.84         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MK 
      122.17        86.14        18.12        41.23        28.18        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A875 
       15.52        15.81        41.42        44.91        25.78        75.91 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H 
       97.41        23.93        85.18        55.56        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       37.05        38.04        42.08         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       25.48         4.87        52.96        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SK 
       60.56        16.83        41.46        45.14        28.77        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI 
       32.45       114.38        71.34        62.79         8.98        53.36 
TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99         3.09        14.53        13.28        10.13 

  TP53 MUTATED TP53 WILD-TYPE 
          0.92           0.72 
  TP53 MUTATED TP53 WILD-TYPE 
        115.86         165.17 
  TP53 MUTATED TP53 WILD-TYPE 
        34.685         27.020 
[1] "0.9 - 115.9 (34.7)" "0.7 - 165.2 (27.0)"
[1] "hr=" "2.2"
D2V2, continuous
                vv
clus              T2  T3  T4
  TP53 MUTATED    11  30   1
  TP53 WILD-TYPE 161 209   5
D2V3, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T2           11            161
  T3           30            209
  T4            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"
D2V4, binary
                cls
clus               0   1
  TP53 MUTATED    32  10
  TP53 WILD-TYPE 267  48
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     32   10
  TP53 WILD-TYPE  267   48
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           32            267
  1           10             48
[1] 2 2
[1] FALSE
D2V5, binary
                cls
clus               0   1
  TP53 MUTATED     2  40
  TP53 WILD-TYPE  13 365
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      2   40
  TP53 WILD-TYPE   13  365
                                        clus
vv                                       TP53 MUTATED TP53 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            2             13
  PROSTATE ADENOCARCINOMA ACINAR TYPE              40            365
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  TP53 MUTATED    27  15   0   0
  TP53 WILD-TYPE 256  88   5  15
D2V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           27            256
  R1           15             88
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, continuous
D2V8, continuous
D2V9, continuous
D2V10, continuous
D2V11, continuous
D2V12, continuous
D2V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0    12
  TP53 WILD-TYPE     2                         7   135
D2V14, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                               12            135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = PTEN MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    14   0
  PTEN WILD-TYPE 398   7
  PTEN MUTATED PTEN WILD-TYPE 
            14            405 
  PTEN MUTATED PTEN WILD-TYPE 
             0              7 
$`PTEN MUTATED`
TCGA-CH-5737 TCGA-CH-5740 TCGA-CH-5791 TCGA-EJ-7791 TCGA-EJ-A65D TCGA-FC-7961 
        2.99         1.02        33.01        19.59        12.92        15.42 
TCGA-G9-6366 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-A6AL TCGA-KC-A4BV TCGA-KK-A6E1 
        3.32        28.60         1.68         2.20        43.66        54.54 
TCGA-KK-A6E7 TCGA-KK-A8I6 
       67.07        21.96 

$`PTEN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
       25.35         6.97        22.06        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5792 TCGA-CH-5794 
       15.98        26.99         9.99        32.02         2.99        29.00 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.53        14.14        18.15        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       21.96        23.34        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB 
        9.83         8.75         4.54        28.41        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 
       47.44        45.30        39.39        44.81        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 
       36.36        37.35        14.47        28.54         0.79        40.08 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94        67.99       101.79        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        41.42        44.91        25.78       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         2.99        31.99        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW 
        8.98        14.04        53.36        60.99        62.37         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  PTEN MUTATED PTEN WILD-TYPE 
          1.02           0.72 
  PTEN MUTATED PTEN WILD-TYPE 
         67.07         165.17 
  PTEN MUTATED PTEN WILD-TYPE 
        17.505         27.580 
[1] "1.0 - 67.1 (17.5)"  "0.7 - 165.2 (27.6)"
[1] "hr="     "9200000"
D3V2, continuous
                vv
clus              T2  T3  T4
  PTEN MUTATED     6   8   0
  PTEN WILD-TYPE 166 231   6
D3V3, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T2            6            166
  T3            8            231
  T4            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"
D3V4, binary
                cls
clus               0   1
  PTEN MUTATED    11   2
  PTEN WILD-TYPE 288  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     11    2
  PTEN WILD-TYPE  288   56
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0           11            288
  1            2             56
[1] 2 2
[1] FALSE
D3V5, binary
                cls
clus               0   1
  PTEN MUTATED     1  13
  PTEN WILD-TYPE  14 392
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1   13
  PTEN WILD-TYPE   14  392
                                        clus
vv                                       PTEN MUTATED PTEN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE              13            392
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  PTEN MUTATED     9   2   0   1
  PTEN WILD-TYPE 274 101   5  14
D3V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            9            274
  R1            2            101
  R2            0              5
  RX            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, continuous
D3V8, continuous
D3V9, continuous
D3V10, continuous
D3V11, continuous
D3V12, continuous
D3V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         0     8
  PTEN WILD-TYPE     2                         7   139
D3V14, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                8            139
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = CTNNB1 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2                0   1
  CTNNB1 MUTATED    11   0
  CTNNB1 WILD-TYPE 401   7
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              11              408 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
               0                7 
$`CTNNB1 MUTATED`
TCGA-CH-5752 TCGA-EJ-5494 TCGA-EJ-5525 TCGA-EJ-A65D TCGA-HC-7212 TCGA-HC-7738 
       31.00        27.16        36.66        12.92        28.60        31.69 
TCGA-HC-8262 TCGA-KK-A6DY TCGA-M7-A722 TCGA-QU-A6IM TCGA-VP-A87H 
       22.32       115.86        34.85        41.00        21.80 

$`CTNNB1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       35.01         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        2.99        29.00        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       64.50        51.88        68.35        43.07        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        23.34        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        9.27         9.83         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
       44.55         0.72         2.10        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       17.95         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       23.67        14.37        20.28        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40        77.72        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 
        5.19        21.14        12.62        13.15        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         3.19       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           12.92             0.72 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          115.86           165.17 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
           31.00            27.14 
[1] "12.9 - 115.9 (31.0)" "0.7 - 165.2 (27.1)" 
[1] "hr="     "8.3e+07"
D4V2, continuous
                  vv
clus                T2  T3  T4
  CTNNB1 MUTATED     6   5   0
  CTNNB1 WILD-TYPE 166 234   6
D4V3, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T2              6              166
  T3              5              234
  T4              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"
D4V4, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED    10   0
  CTNNB1 WILD-TYPE 289  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     10    0
  CTNNB1 WILD-TYPE  289   58
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             10              289
  1              0               58
[1] 2 2
[1] FALSE
D4V5, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     1  10
  CTNNB1 WILD-TYPE  14 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1   10
  CTNNB1 WILD-TYPE   14  395
                                        clus
vv                                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1               14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                10              395
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CTNNB1 MUTATED     7   2   1   0
  CTNNB1 WILD-TYPE 276 101   4  15
D4V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0              7              276
  R1              2              101
  R2              1                4
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, continuous
D4V8, continuous
D4V9, continuous
D4V10, continuous
D4V11, continuous
D4V12, continuous
D4V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED       0                         0     5
  CTNNB1 WILD-TYPE     2                         7   142
D4V14, multiclass
                           clus
vv                          CTNNB1 MUTATED CTNNB1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = FOXA1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  FOXA1 MUTATED    25   0
  FOXA1 WILD-TYPE 387   7
  FOXA1 MUTATED FOXA1 WILD-TYPE 
             25             394 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              0               7 
$`FOXA1 MUTATED`
TCGA-2A-A8VX TCGA-2A-A8W1 TCGA-CH-5737 TCGA-EJ-5494 TCGA-EJ-7330 TCGA-EJ-7782 
       33.96         3.68         2.99        27.16         6.28        38.37 
TCGA-EJ-7789 TCGA-G9-6351 TCGA-HC-7210 TCGA-HC-8265 TCGA-HC-A6AO TCGA-HC-A6AP 
       18.15        46.16        28.54        15.88        17.42         2.33 
TCGA-J9-A8CP TCGA-KC-A7F5 TCGA-KK-A8IB TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IK 
       12.69         2.99         2.73        26.43        82.36        51.39 
TCGA-M7-A722 TCGA-QU-A6IL TCGA-QU-A6IN TCGA-V1-A8MM TCGA-YJ-A8SW TCGA-YL-A8S9 
       34.85         3.19       140.19        39.29         4.87        60.56 
TCGA-YL-A9WI 
       53.36 

$`FOXA1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W3 TCGA-CH-5738 
       20.42        43.79        32.71        22.06        25.35         6.97 
TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 
       22.06         1.02        12.99        13.97         1.97         2.99 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        13.02        35.01        31.00         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        13.02        15.98 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.99         9.99        32.02        33.01         2.99        29.00 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       33.11        19.56        13.32        29.79        46.52        44.88 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
       26.30        45.73        28.93        30.31        27.19        23.90 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       38.93        48.13        36.69        48.53        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       60.23        46.55        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 
       27.09        35.18        30.35        27.68        24.39        23.90 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 
       25.87        25.68        20.55        14.53        14.14        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       37.35        14.47         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        1.61         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
       10.78        23.67        14.37        20.28        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-KC-A4BL 
        6.97        10.62        13.32        15.22        40.67        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F6 
       59.67        19.96        44.35        43.66        21.86         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       63.48        67.43        69.27        66.18       113.98        51.25 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP 
       25.08        29.23        18.84        41.00       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
        2.99        31.99        25.48        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        71.77        62.14        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         8.98        14.04        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  FOXA1 MUTATED FOXA1 WILD-TYPE 
           2.33            0.72 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
         140.19          165.17 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
         26.430          27.485 
[1] "2.3 - 140.2 (26.4)" "0.7 - 165.2 (27.5)"
[1] "hr="     "8.1e+07"
D5V2, continuous
                 vv
clus               T2  T3  T4
  FOXA1 MUTATED    10  15   0
  FOXA1 WILD-TYPE 162 224   6
D5V3, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  T2            10             162
  T3            15             224
  T4             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"
D5V4, binary
                 cls
clus                0   1
  FOXA1 MUTATED    20   1
  FOXA1 WILD-TYPE 279  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED     20    1
  FOXA1 WILD-TYPE  279   57
   clus
vv  FOXA1 MUTATED FOXA1 WILD-TYPE
  0            20             279
  1             1              57
[1] 2 2
[1] FALSE
D5V5, binary
                 cls
clus                0   1
  FOXA1 MUTATED     1  24
  FOXA1 WILD-TYPE  14 381
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      1   24
  FOXA1 WILD-TYPE   14  381
                                        clus
vv                                       FOXA1 MUTATED FOXA1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1              14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               24             381
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  FOXA1 MUTATED    17   7   0   1
  FOXA1 WILD-TYPE 266  96   5  14
D5V6, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  R0            17             266
  R1             7              96
  R2             0               5
  RX             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, continuous
D5V8, continuous
D5V9, continuous
D5V10, continuous
D5V11, continuous
D5V12, continuous
D5V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXA1 MUTATED       0                         2     5
  FOXA1 WILD-TYPE     2                         5   142
D5V14, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               5
  WHITE                                 5             142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = ATM MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  ATM MUTATED    18   1
  ATM WILD-TYPE 394   6
  ATM MUTATED ATM WILD-TYPE 
           19           400 
  ATM MUTATED ATM WILD-TYPE 
            1             6 
$`ATM MUTATED`
TCGA-CH-5737 TCGA-CH-5762 TCGA-EJ-5507 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7783 
        2.99        44.02        23.90        48.53        52.27        25.87 
TCGA-EJ-7784 TCGA-G9-7510 TCGA-G9-7521 TCGA-HC-8260 TCGA-HC-A4ZV TCGA-J4-A67Q 
       25.68        38.96        30.97        22.55         0.76        32.05 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-M7-A725 TCGA-VN-A88K TCGA-YL-A8S9 TCGA-YL-A8SC 
       26.43        82.36        18.84        25.51        60.56        41.46 
TCGA-YL-A8SH 
       28.77 

$`ATM WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
       25.35         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5763 TCGA-CH-5764 
       31.00         1.02         2.04         0.92        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 
       27.19        38.93        48.13        36.69        38.53        36.23 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       60.23        46.55        47.80        64.50        51.88        68.35 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       43.07        36.66        38.76        39.75        60.23        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       38.37        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7519 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.17         2.27        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
        1.15        22.36         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67R TCGA-J4-A67S 
       25.32        30.94        16.54        27.58        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
       10.78        23.67        14.37        20.28        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        6.97        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
        2.99         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       29.23         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8SA TCGA-YL-A8SB 
       51.45        48.72        71.77        62.14        16.83        56.52 
TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  ATM MUTATED ATM WILD-TYPE 
         0.76          0.72 
  ATM MUTATED ATM WILD-TYPE 
        82.36        165.17 
  ATM MUTATED ATM WILD-TYPE 
        28.77         27.24 
[1] "0.8 - 82.4 (28.8)"  "0.7 - 165.2 (27.2)"
[1] "hr=" "5.3"
D6V2, continuous
               vv
clus             T2  T3  T4
  ATM MUTATED     4  14   1
  ATM WILD-TYPE 168 225   5
D6V3, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T2           4           168
  T3          14           225
  T4           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"
D6V4, binary
               cls
clus              0   1
  ATM MUTATED    15   3
  ATM WILD-TYPE 284  55
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED     15    3
  ATM WILD-TYPE  284   55
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0          15           284
  1           3            55
[1] 2 2
[1] FALSE
D6V5, binary
               cls
clus              0   1
  ATM MUTATED     0  19
  ATM WILD-TYPE  15 386
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      0   19
  ATM WILD-TYPE   15  386
                                        clus
vv                                       ATM MUTATED ATM WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE           0            15
  PROSTATE ADENOCARCINOMA ACINAR TYPE             19           386
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  ATM MUTATED     9   9   0   0
  ATM WILD-TYPE 274  94   5  15
D6V6, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  R0           9           274
  R1           9            94
  R2           0             5
  RX           0            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, continuous
D6V8, continuous
D6V9, continuous
D6V10, continuous
D6V11, continuous
D6V12, continuous
D6V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         1     6
  ATM WILD-TYPE     2                         6   141
D6V14, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           1             6
  WHITE                               6           141
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = PIK3CA MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED    11   0
  PIK3CA WILD-TYPE 401   7
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              11              408 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0                7 
$`PIK3CA MUTATED`
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-8469 TCGA-EJ-A65D TCGA-HC-7078 TCGA-HC-7081 
       36.66        38.76        76.41        12.92        65.26        37.35 
TCGA-HC-7231 TCGA-HC-A6AN TCGA-J9-A8CL TCGA-QU-A6IN TCGA-VP-A87H 
        2.37         1.61        13.32       140.19        21.80 

$`PIK3CA WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 
        3.75        23.05        19.92        77.16        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       23.80        21.96        23.34        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        9.27         9.83         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
       19.76         2.93        36.36        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       28.60        40.08         1.68        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        1.78         2.01         2.20        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         3.19        41.00       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            1.61             0.72 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          140.19           165.17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           36.66            27.24 
[1] "1.6 - 140.2 (36.7)" "0.7 - 165.2 (27.2)"
[1] "hr="     "8.3e+07"
D7V2, continuous
                  vv
clus                T2  T3  T4
  PIK3CA MUTATED     3   8   0
  PIK3CA WILD-TYPE 169 231   6
D7V3, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T2              3              169
  T3              8              231
  T4              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"
D7V4, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     7   1
  PIK3CA WILD-TYPE 292  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    1
  PIK3CA WILD-TYPE  292   57
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0              7              292
  1              1               57
[1] 2 2
[1] FALSE
D7V5, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  10
  PIK3CA WILD-TYPE  14 395
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   10
  PIK3CA WILD-TYPE   14  395
                                        clus
vv                                       PIK3CA MUTATED PIK3CA WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1               14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                10              395
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED     6   2   2   1
  PIK3CA WILD-TYPE 277 101   3  14
D7V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0              6              277
  R1              2              101
  R2              2                3
  RX              1               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, continuous
D7V8, continuous
D7V9, continuous
D7V10, continuous
D7V11, continuous
D7V12, continuous
D7V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         0     5
  PIK3CA WILD-TYPE     2                         7   142
D7V14, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = BRAF MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  BRAF MUTATED     8   0
  BRAF WILD-TYPE 404   7
  BRAF MUTATED BRAF WILD-TYPE 
             8            411 
  BRAF MUTATED BRAF WILD-TYPE 
             0              7 
$`BRAF MUTATED`
TCGA-EJ-5505 TCGA-EJ-A65E TCGA-G9-6498 TCGA-HC-7742 TCGA-KC-A4BN TCGA-KK-A59V 
       30.31        13.71        64.18         1.48        59.67       113.10 
TCGA-V1-A8MU TCGA-ZG-A8QY 
       53.16        13.28 

$`BRAF WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       28.93        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       27.29        58.22        56.75        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       40.67        12.69        30.71        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN 
       40.44        16.70        14.73        39.29        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       15.58        22.55         6.64         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL 
       42.08        48.03         9.04         2.99        31.99        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
        3.09        14.53        10.13 

  BRAF MUTATED BRAF WILD-TYPE 
          1.48           0.72 
  BRAF MUTATED BRAF WILD-TYPE 
        113.10         165.17 
  BRAF MUTATED BRAF WILD-TYPE 
        41.735         27.190 
[1] "1.5 - 113.1 (41.7)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9300000"
D8V2, continuous
                vv
clus              T2  T3  T4
  BRAF MUTATED     2   6   0
  BRAF WILD-TYPE 170 233   6
D8V3, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  T2            2            170
  T3            6            233
  T4            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"
D8V4, binary
                cls
clus               0   1
  BRAF MUTATED     5   2
  BRAF WILD-TYPE 294  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      5    2
  BRAF WILD-TYPE  294   56
   clus
vv  BRAF MUTATED BRAF WILD-TYPE
  0            5            294
  1            2             56
[1] 2 2
[1] FALSE
D8V5, binary
                cls
clus               0   1
  BRAF MUTATED     1   7
  BRAF WILD-TYPE  14 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      1    7
  BRAF WILD-TYPE   14  398
                                        clus
vv                                       BRAF MUTATED BRAF WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               7            398
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED     5   2   0   1
  BRAF WILD-TYPE 278 101   5  14
D8V6, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0            5            278
  R1            2            101
  R2            0              5
  RX            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, continuous
D8V8, continuous
D8V9, continuous
D8V10, continuous
D8V11, continuous
D8V12, continuous
D8V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BRAF MUTATED       0                         0     2
  BRAF WILD-TYPE     2                         7   145
D8V14, multiclass
[1] "Remove cluster labels:" "BRAF MUTATED"          
clus
  BRAF MUTATED BRAF WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7314 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7231     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7744 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818     TCGA-HC-7819 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" 

Clustering(9) Variable = HRAS MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  HRAS MUTATED     5   0
  HRAS WILD-TYPE 407   7
  HRAS MUTATED HRAS WILD-TYPE 
             5            414 
  HRAS MUTATED HRAS WILD-TYPE 
             0              7 
$`HRAS MUTATED`
TCGA-EJ-A7NJ TCGA-G9-6361 TCGA-HC-7817 TCGA-HI-7168 TCGA-VN-A88N 
        6.48        46.52        30.51        78.61        15.52 

$`HRAS WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NK 
       11.61        28.70         8.22        14.20        15.58        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6362 TCGA-G9-6363 
       46.16        50.70        49.35        47.15        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7818 TCGA-HC-7819 
       26.04         1.97        17.16        25.71        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       18.84        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88O TCGA-VN-A88P 
        8.84        25.51        24.53         6.21        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  HRAS MUTATED HRAS WILD-TYPE 
          6.48           0.72 
  HRAS MUTATED HRAS WILD-TYPE 
         78.61         165.17 
  HRAS MUTATED HRAS WILD-TYPE 
         30.51          27.24 
[1] "6.5 - 78.6 (30.5)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D9V2, continuous
                vv
clus              T2  T3  T4
  HRAS MUTATED     2   3   0
  HRAS WILD-TYPE 170 236   6
D9V3, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  T2            2            170
  T3            3            236
  T4            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"
D9V4, binary
                cls
clus               0   1
  HRAS MUTATED     4   0
  HRAS WILD-TYPE 295  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      4    0
  HRAS WILD-TYPE  295   58
   clus
vv  HRAS MUTATED HRAS WILD-TYPE
  0            4            295
  1            0             58
[1] 2 2
[1] FALSE
D9V5, binary
                cls
clus               0   1
  HRAS MUTATED     0   5
  HRAS WILD-TYPE  15 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0    5
  HRAS WILD-TYPE   15  400
                                        clus
vv                                       HRAS MUTATED HRAS WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               5            400
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  HRAS MUTATED     3   1   0   0
  HRAS WILD-TYPE 280 102   5  15
D9V6, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  R0            3            280
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, continuous
D9V8, continuous
D9V9, continuous
D9V10, continuous
D9V11, continuous
D9V12, continuous
D9V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       0                         0     2
  HRAS WILD-TYPE     2                         7   145
D9V14, multiclass
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6353     TCGA-G9-6356     TCGA-G9-6362     TCGA-G9-6363 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7231     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7169 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" 

Clustering(10) Variable = KDM6A MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2               0   1
  KDM6A MUTATED     9   0
  KDM6A WILD-TYPE 403   7
  KDM6A MUTATED KDM6A WILD-TYPE 
              9             410 
  KDM6A MUTATED KDM6A WILD-TYPE 
              0               7 
$`KDM6A MUTATED`
TCGA-EJ-5509 TCGA-EJ-7317 TCGA-EJ-7331 TCGA-EJ-A65G TCGA-HC-7212 TCGA-KK-A6E8 
       48.13        25.35        24.39        21.90        28.60        58.19 
TCGA-V1-A8ML TCGA-XA-A8JR TCGA-YL-A9WK 
       14.73         3.91        62.37 

$`KDM6A WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 
       28.93        30.31        27.19        23.90        38.93        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       33.14        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        9.27         9.83         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
       28.54         0.79        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
      113.33        67.07         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       40.44        16.70        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       15.58        22.55         6.64         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       14.76        45.47        32.19        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         2.99        31.99        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-ZG-A8QW TCGA-ZG-A8QX 
        8.98        14.04        53.36        60.99         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  KDM6A MUTATED KDM6A WILD-TYPE 
           3.91            0.72 
  KDM6A MUTATED KDM6A WILD-TYPE 
          62.37          165.17 
  KDM6A MUTATED KDM6A WILD-TYPE 
          25.35           27.34 
[1] "3.9 - 62.4 (25.4)"  "0.7 - 165.2 (27.3)"
[1] "hr="     "9200000"
D10V2, continuous
                 vv
clus               T2  T3  T4
  KDM6A MUTATED     8   1   0
  KDM6A WILD-TYPE 164 238   6
D10V3, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  T2             8             164
  T3             1             238
  T4             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"
D10V4, binary
                 cls
clus                0   1
  KDM6A MUTATED     9   0
  KDM6A WILD-TYPE 290  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      9    0
  KDM6A WILD-TYPE  290   58
   clus
vv  KDM6A MUTATED KDM6A WILD-TYPE
  0             9             290
  1             0              58
[1] 2 2
[1] FALSE
D10V5, binary
                 cls
clus                0   1
  KDM6A MUTATED     0   9
  KDM6A WILD-TYPE  15 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      0    9
  KDM6A WILD-TYPE   15  396
                                        clus
vv                                       KDM6A MUTATED KDM6A WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                9             396
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  KDM6A MUTATED     5   1   1   1
  KDM6A WILD-TYPE 278 102   4  14
D10V6, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  R0             5             278
  R1             1             102
  R2             1               4
  RX             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, continuous
D10V8, continuous
D10V9, continuous
D10V10, continuous
D10V11, continuous
D10V12, continuous
D10V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       0                         0     4
  KDM6A WILD-TYPE     2                         7   143
D10V14, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = IDH1 MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  IDH1 MUTATED     5   0
  IDH1 WILD-TYPE 407   7
  IDH1 MUTATED IDH1 WILD-TYPE 
             5            414 
  IDH1 MUTATED IDH1 WILD-TYPE 
             0              7 
$`IDH1 MUTATED`
TCGA-CH-5772 TCGA-EJ-7125 TCGA-G9-7523 TCGA-KK-A6E7 TCGA-M7-A722 
       15.98        93.70        28.18        67.07        34.85 

$`IDH1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       88.34        74.10        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        30.97        35.34        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
      115.13        49.25       113.33        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       12.62        13.15        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  IDH1 MUTATED IDH1 WILD-TYPE 
         15.98           0.72 
  IDH1 MUTATED IDH1 WILD-TYPE 
         93.70         165.17 
  IDH1 MUTATED IDH1 WILD-TYPE 
        34.850         27.175 
[1] "16.0 - 93.7 (34.9)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9200000"
D11V2, continuous
                vv
clus              T2  T3  T4
  IDH1 MUTATED     1   4   0
  IDH1 WILD-TYPE 171 235   6
D11V3, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  T2            1            171
  T3            4            235
  T4            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"
D11V4, binary
                cls
clus               0   1
  IDH1 MUTATED     4   1
  IDH1 WILD-TYPE 295  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      4    1
  IDH1 WILD-TYPE  295   57
   clus
vv  IDH1 MUTATED IDH1 WILD-TYPE
  0            4            295
  1            1             57
[1] 2 2
[1] FALSE
D11V5, binary
                cls
clus               0   1
  IDH1 MUTATED     0   5
  IDH1 WILD-TYPE  15 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  IDH1 MUTATED      0    5
  IDH1 WILD-TYPE   15  400
                                        clus
vv                                       IDH1 MUTATED IDH1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               5            400
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  IDH1 MUTATED     1   4   0   0
  IDH1 WILD-TYPE 282  99   5  15
D11V6, multiclass
    clus
vv   IDH1 MUTATED IDH1 WILD-TYPE
  R0            1            282
  R1            4             99
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, continuous
D11V8, continuous
D11V9, continuous
D11V10, continuous
D11V11, continuous
D11V12, continuous
D11V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IDH1 MUTATED       0                         0     2
  IDH1 WILD-TYPE     2                         7   145
D11V14, multiclass
[1] "Remove cluster labels:" "IDH1 MUTATED"          
clus
  IDH1 MUTATED IDH1 WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5494 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497     TCGA-EJ-5498 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5504 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7314     TCGA-EJ-7315 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332     TCGA-G9-6333 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342     TCGA-G9-6343 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818     TCGA-HC-7819 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"IDH1 WILD-TYPE" "IDH1 WILD-TYPE" 

Clustering(12) Variable = SMG7 MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  SMG7 MUTATED     7   0
  SMG7 WILD-TYPE 405   7
  SMG7 MUTATED SMG7 WILD-TYPE 
             7            412 
  SMG7 MUTATED SMG7 WILD-TYPE 
             0              7 
$`SMG7 MUTATED`
TCGA-2A-A8VX TCGA-CH-5737 TCGA-EJ-7325 TCGA-EJ-A8FS TCGA-HC-7742 TCGA-HI-7169 
       33.96         2.99        35.18         8.75         1.48        88.24 
TCGA-KK-A59V 
      113.10 

$`SMG7 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        6.97        22.06         1.02        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       25.35        33.83        27.09        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
       10.82         9.27         9.83         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
       10.78        23.67        14.37        20.28        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        6.97        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
        2.99         8.65        19.66         8.88        11.57        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        86.40        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF 
       32.91        63.48         2.73        67.43        69.27        26.43 
TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL 
       82.36        66.18       113.98        51.25        51.39        20.65 
TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 
       47.28         5.19        21.14        12.62        13.15        34.85 
TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN 
       25.08        29.23        18.84         3.19        41.00       140.19 
TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ 
      122.17        86.14        18.12        41.23        28.18        40.44 
TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN 
       16.70        14.73        39.29        53.16        52.08        30.38 
TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L 
       15.58        22.55         6.64         8.84        25.51        24.53 
TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R 
        6.21        15.52        15.81        41.42        44.91        25.78 
TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B 
      111.39        75.91       109.58        97.41        23.93        85.18 
TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K 
       55.56        60.92        66.97        21.80        53.36        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL 
       42.08        48.03         9.04         2.99        31.99        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  SMG7 MUTATED SMG7 WILD-TYPE 
          1.48           0.72 
  SMG7 MUTATED SMG7 WILD-TYPE 
        113.10         165.17 
  SMG7 MUTATED SMG7 WILD-TYPE 
         33.96          27.24 
[1] "1.5 - 113.1 (34.0)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9200000"
D12V2, continuous
                vv
clus              T2  T3  T4
  SMG7 MUTATED     1   6   0
  SMG7 WILD-TYPE 171 233   6
D12V3, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  T2            1            171
  T3            6            233
  T4            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"
D12V4, binary
                cls
clus               0   1
  SMG7 MUTATED     7   0
  SMG7 WILD-TYPE 292  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      7    0
  SMG7 WILD-TYPE  292   58
   clus
vv  SMG7 MUTATED SMG7 WILD-TYPE
  0            7            292
  1            0             58
[1] 2 2
[1] FALSE
D12V5, binary
                cls
clus               0   1
  SMG7 MUTATED     0   7
  SMG7 WILD-TYPE  15 398
[1] "tbl2"
                cls
clus             [,1] [,2]
  SMG7 MUTATED      0    7
  SMG7 WILD-TYPE   15  398
                                        clus
vv                                       SMG7 MUTATED SMG7 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               7            398
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  SMG7 MUTATED     6   1   0   0
  SMG7 WILD-TYPE 277 102   5  15
D12V6, multiclass
    clus
vv   SMG7 MUTATED SMG7 WILD-TYPE
  R0            6            277
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, continuous
D12V8, continuous
D12V9, continuous
D12V10, continuous
D12V11, continuous
D12V12, continuous
D12V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SMG7 MUTATED       0                         0     3
  SMG7 WILD-TYPE     2                         7   144
D12V14, multiclass
                           clus
vv                          SMG7 MUTATED SMG7 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = ZMYM3 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2               0   1
  ZMYM3 MUTATED     9   0
  ZMYM3 WILD-TYPE 403   7
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              9             410 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
              0               7 
$`ZMYM3 MUTATED`
TCGA-CH-5741 TCGA-CH-5772 TCGA-G9-6362 TCGA-HC-A76W TCGA-KC-A4BV TCGA-KK-A59V 
       12.99        15.98        47.44         7.00        43.66       113.10 
TCGA-KK-A6E2 TCGA-KK-A7AP TCGA-KK-A7B2 
      165.17         6.44        36.13 

$`ZMYM3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5743 
       25.35         2.99         6.97        22.06         1.02        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       13.02        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        1.25         4.41         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
       54.54        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       49.94        32.84        34.95        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
           6.44            0.72 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
         165.17          140.19 
  ZMYM3 MUTATED ZMYM3 WILD-TYPE 
          36.13           27.24 
[1] "6.4 - 165.2 (36.1)" "0.7 - 140.2 (27.2)"
[1] "hr="     "8.3e+07"
D13V2, continuous
                 vv
clus               T2  T3  T4
  ZMYM3 MUTATED     1   8   0
  ZMYM3 WILD-TYPE 171 231   6
D13V3, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  T2             1             171
  T3             8             231
  T4             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"
D13V4, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     6   3
  ZMYM3 WILD-TYPE 293  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      6    3
  ZMYM3 WILD-TYPE  293   55
   clus
vv  ZMYM3 MUTATED ZMYM3 WILD-TYPE
  0             6             293
  1             3              55
[1] 2 2
[1] FALSE
D13V5, binary
                 cls
clus                0   1
  ZMYM3 MUTATED     0   9
  ZMYM3 WILD-TYPE  15 396
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZMYM3 MUTATED      0    9
  ZMYM3 WILD-TYPE   15  396
                                        clus
vv                                       ZMYM3 MUTATED ZMYM3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                9             396
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZMYM3 MUTATED     4   5   0   0
  ZMYM3 WILD-TYPE 279  98   5  15
D13V6, multiclass
    clus
vv   ZMYM3 MUTATED ZMYM3 WILD-TYPE
  R0             4             279
  R1             5              98
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, continuous
D13V8, continuous
D13V9, continuous
D13V10, continuous
D13V11, continuous
D13V12, continuous
D13V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZMYM3 MUTATED       0                         0     3
  ZMYM3 WILD-TYPE     2                         7   144
D13V14, multiclass
                           clus
vv                          ZMYM3 MUTATED ZMYM3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = EHHADH MUTATION ANALYSIS
D14V1, survival
                  sevent
clus2                0   1
  EHHADH MUTATED     5   0
  EHHADH WILD-TYPE 407   7
  EHHADH MUTATED EHHADH WILD-TYPE 
               5              414 
  EHHADH MUTATED EHHADH WILD-TYPE 
               0                7 
$`EHHADH MUTATED`
TCGA-CH-5752 TCGA-HC-7745 TCGA-V1-A8MU TCGA-VP-A87B TCGA-YL-A8SC 
       31.00        23.70        53.16        85.18        41.46 

$`EHHADH WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       35.01         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7747 
        2.10        31.69        23.57         1.48         1.68        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        39.29        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      109.58        97.41        23.93        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       56.52        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  EHHADH MUTATED EHHADH WILD-TYPE 
           23.70             0.72 
  EHHADH MUTATED EHHADH WILD-TYPE 
           85.18           165.17 
  EHHADH MUTATED EHHADH WILD-TYPE 
          41.460           27.175 
[1] "23.7 - 85.2 (41.5)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9200000"
D14V2, continuous
                  vv
clus                T2  T3  T4
  EHHADH MUTATED     1   4   0
  EHHADH WILD-TYPE 171 235   6
D14V3, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  T2              1              171
  T3              4              235
  T4              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"
D14V4, binary
                  cls
clus                 0   1
  EHHADH MUTATED     4   1
  EHHADH WILD-TYPE 295  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      4    1
  EHHADH WILD-TYPE  295   57
   clus
vv  EHHADH MUTATED EHHADH WILD-TYPE
  0              4              295
  1              1               57
[1] 2 2
[1] FALSE
D14V5, binary
                  cls
clus                 0   1
  EHHADH MUTATED     0   5
  EHHADH WILD-TYPE  15 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EHHADH MUTATED      0    5
  EHHADH WILD-TYPE   15  400
                                        clus
vv                                       EHHADH MUTATED EHHADH WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              400
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  EHHADH MUTATED     3   2   0   0
  EHHADH WILD-TYPE 280 101   5  15
D14V6, multiclass
    clus
vv   EHHADH MUTATED EHHADH WILD-TYPE
  R0              3              280
  R1              2              101
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, continuous
D14V8, continuous
D14V9, continuous
D14V10, continuous
D14V11, continuous
D14V12, continuous
D14V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EHHADH MUTATED       0                         0     2
  EHHADH WILD-TYPE     2                         7   145
D14V14, multiclass
[1] "Remove cluster labels:" "EHHADH MUTATED"        
clus
  EHHADH MUTATED EHHADH WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5494 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497       TCGA-EJ-5498 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125       TCGA-EJ-7314 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7327 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331       TCGA-EJ-7781 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"EHHADH WILD-TYPE" "EHHADH WILD-TYPE" 

Clustering(15) Variable = TP53BP1 MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  TP53BP1 MUTATED     7   0
  TP53BP1 WILD-TYPE 405   7
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                7               412 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                0                 7 
$`TP53BP1 MUTATED`
TCGA-EJ-7786 TCGA-FC-A4JI TCGA-G9-6338 TCGA-J9-A52C TCGA-KK-A59V TCGA-KK-A7B3 
       14.53        13.45        66.67         5.85       113.10        29.56 
TCGA-YL-A8SK 
       46.29 

$`TP53BP1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        25.68        20.55        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
        4.54        28.41        15.42        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6339 
        1.78        41.62        87.35        81.04        67.99        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       20.28        13.87         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
       11.57        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       36.13        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       45.14        28.77        45.86        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
             5.85              0.72 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
           113.10            165.17 
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
            29.56             27.24 
[1] "5.8 - 113.1 (29.6)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9300000"
D15V2, continuous
                   vv
clus                 T2  T3  T4
  TP53BP1 MUTATED     1   6   0
  TP53BP1 WILD-TYPE 171 233   6
D15V3, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  T2               1               171
  T3               6               233
  T4               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"
D15V4, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     4   1
  TP53BP1 WILD-TYPE 295  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      4    1
  TP53BP1 WILD-TYPE  295   57
   clus
vv  TP53BP1 MUTATED TP53BP1 WILD-TYPE
  0               4               295
  1               1                57
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                  0   1
  TP53BP1 MUTATED     0   7
  TP53BP1 WILD-TYPE  15 398
[1] "tbl2"
                   cls
clus                [,1] [,2]
  TP53BP1 MUTATED      0    7
  TP53BP1 WILD-TYPE   15  398
                                        clus
vv                                       TP53BP1 MUTATED TP53BP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  7               398
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  TP53BP1 MUTATED     5   2   0   0
  TP53BP1 WILD-TYPE 278 101   5  15
D15V6, multiclass
    clus
vv   TP53BP1 MUTATED TP53BP1 WILD-TYPE
  R0               5               278
  R1               2               101
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, continuous
D15V8, continuous
D15V9, continuous
D15V10, continuous
D15V11, continuous
D15V12, continuous
D15V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53BP1 MUTATED       0                         0     2
  TP53BP1 WILD-TYPE     2                         7   145
D15V14, multiclass
[1] "Remove cluster labels:" "TP53BP1 MUTATED"       
clus
  TP53BP1 MUTATED TP53BP1 WILD-TYPE 
                2               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6342        TCGA-G9-6343 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353        TCGA-G9-6356 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367        TCGA-G9-6369 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373        TCGA-G9-6377 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775        TCGA-HC-7075 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7231 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"TP53BP1 WILD-TYPE" "TP53BP1 WILD-TYPE" 

Clustering(16) Variable = CNTNAP1 MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  CNTNAP1 MUTATED     7   0
  CNTNAP1 WILD-TYPE 405   7
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                7               412 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
                0                 7 
$`CNTNAP1 MUTATED`
TCGA-EJ-A65M TCGA-HC-8256 TCGA-HC-8265 TCGA-HC-8266 TCGA-J9-A52D TCGA-KC-A7F6 
        7.56        28.27        15.88         1.15         6.97         8.65 
TCGA-XJ-A9DX 
       31.99 

$`CNTNAP1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A6RA 
       12.92        13.71        18.41        21.90        14.83        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.58        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
       13.87         5.85        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
       21.86         2.99        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-Y6-A8TL 
       38.04        42.08        48.03         9.04         2.99        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
             1.15              0.72 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
            31.99            165.17 
  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE 
            8.650            27.485 
[1] "1.1 - 32.0 (8.7)"   "0.7 - 165.2 (27.5)"
[1] "hr="     "3300000"
D16V2, continuous
                   vv
clus                 T2  T3  T4
  CNTNAP1 MUTATED     3   4   0
  CNTNAP1 WILD-TYPE 169 235   6
D16V3, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  T2               3               169
  T3               4               235
  T4               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"
D16V4, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     4   1
  CNTNAP1 WILD-TYPE 295  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      4    1
  CNTNAP1 WILD-TYPE  295   57
   clus
vv  CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  0               4               295
  1               1                57
[1] 2 2
[1] FALSE
D16V5, binary
                   cls
clus                  0   1
  CNTNAP1 MUTATED     1   6
  CNTNAP1 WILD-TYPE  14 399
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CNTNAP1 MUTATED      1    6
  CNTNAP1 WILD-TYPE   14  399
                                        clus
vv                                       CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  6               399
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  CNTNAP1 MUTATED     3   3   0   0
  CNTNAP1 WILD-TYPE 280 100   5  15
D16V6, multiclass
    clus
vv   CNTNAP1 MUTATED CNTNAP1 WILD-TYPE
  R0               3               280
  R1               3               100
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, continuous
D16V8, continuous
D16V9, continuous
D16V10, continuous
D16V11, continuous
D16V12, continuous
D16V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CNTNAP1 MUTATED       0                         0     0
  CNTNAP1 WILD-TYPE     2                         7   147
D16V14, multiclass

Clustering(17) Variable = BMP2K MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  BMP2K MUTATED     6   0
  BMP2K WILD-TYPE 406   7
  BMP2K MUTATED BMP2K WILD-TYPE 
              6             413 
  BMP2K MUTATED BMP2K WILD-TYPE 
              0               7 
$`BMP2K MUTATED`
TCGA-EJ-5512 TCGA-EJ-8474 TCGA-G9-6494 TCGA-HC-8259 TCGA-HC-A6AP TCGA-VP-A87J 
       38.53        25.18        58.22         2.27         2.33        53.36 

$`BMP2K WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       27.29        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.17        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
        1.61        17.42         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37         3.09        14.53        13.28        10.13 

  BMP2K MUTATED BMP2K WILD-TYPE 
           2.27            0.72 
  BMP2K MUTATED BMP2K WILD-TYPE 
          58.22          165.17 
  BMP2K MUTATED BMP2K WILD-TYPE 
         31.855          27.290 
[1] "2.3 - 58.2 (31.9)"  "0.7 - 165.2 (27.3)"
[1] "hr="     "9100000"
D17V2, continuous
                 vv
clus               T2  T3  T4
  BMP2K MUTATED     3   2   1
  BMP2K WILD-TYPE 169 237   5
D17V3, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  T2             3             169
  T3             2             237
  T4             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"
D17V4, binary
                 cls
clus                0   1
  BMP2K MUTATED     3   1
  BMP2K WILD-TYPE 296  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      3    1
  BMP2K WILD-TYPE  296   57
   clus
vv  BMP2K MUTATED BMP2K WILD-TYPE
  0             3             296
  1             1              57
[1] 2 2
[1] FALSE
D17V5, binary
                 cls
clus                0   1
  BMP2K MUTATED     0   6
  BMP2K WILD-TYPE  15 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  BMP2K MUTATED      0    6
  BMP2K WILD-TYPE   15  399
                                        clus
vv                                       BMP2K MUTATED BMP2K WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             399
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  BMP2K MUTATED     3   1   1   1
  BMP2K WILD-TYPE 280 102   4  14
D17V6, multiclass
    clus
vv   BMP2K MUTATED BMP2K WILD-TYPE
  R0             3             280
  R1             1             102
  R2             1               4
  RX             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, continuous
D17V8, continuous
D17V9, continuous
D17V10, continuous
D17V11, continuous
D17V12, continuous
D17V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BMP2K MUTATED       0                         0     2
  BMP2K WILD-TYPE     2                         7   145
D17V14, multiclass
[1] "Remove cluster labels:" "BMP2K MUTATED"         
clus
  BMP2K MUTATED BMP2K WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"BMP2K WILD-TYPE" "BMP2K WILD-TYPE" 

Clustering(18) Variable = RPTN MUTATION ANALYSIS
D18V1, survival
                sevent
clus2              0   1
  RPTN MUTATED     6   0
  RPTN WILD-TYPE 406   7
  RPTN MUTATED RPTN WILD-TYPE 
             6            413 
  RPTN MUTATED RPTN WILD-TYPE 
             0              7 
$`RPTN MUTATED`
TCGA-EJ-7782 TCGA-EJ-8469 TCGA-HC-7738 TCGA-HC-7747 TCGA-HC-A6HX TCGA-KK-A59V 
       38.37        76.41        31.69        24.59         1.25       113.10 

$`RPTN WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 
       30.35        27.68         6.28        24.39        23.90        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        77.16        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.48         1.68        23.70        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HY 
        1.61        17.42         2.33         3.48         1.45         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37         3.09        14.53        13.28        10.13 

  RPTN MUTATED RPTN WILD-TYPE 
          1.25           0.72 
  RPTN MUTATED RPTN WILD-TYPE 
        113.10         165.17 
  RPTN MUTATED RPTN WILD-TYPE 
         35.03          27.19 
[1] "1.2 - 113.1 (35.0)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9300000"
D18V2, continuous
                vv
clus              T2  T3  T4
  RPTN MUTATED     4   2   0
  RPTN WILD-TYPE 168 237   6
D18V3, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  T2            4            168
  T3            2            237
  T4            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"
D18V4, binary
                cls
clus               0   1
  RPTN MUTATED     5   0
  RPTN WILD-TYPE 294  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      5    0
  RPTN WILD-TYPE  294   58
   clus
vv  RPTN MUTATED RPTN WILD-TYPE
  0            5            294
  1            0             58
[1] 2 2
[1] FALSE
D18V5, binary
                cls
clus               0   1
  RPTN MUTATED     0   6
  RPTN WILD-TYPE  15 399
[1] "tbl2"
                cls
clus             [,1] [,2]
  RPTN MUTATED      0    6
  RPTN WILD-TYPE   15  399
                                        clus
vv                                       RPTN MUTATED RPTN WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               6            399
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RPTN MUTATED     4   0   0   1
  RPTN WILD-TYPE 279 103   5  14
D18V6, multiclass
    clus
vv   RPTN MUTATED RPTN WILD-TYPE
  R0            4            279
  R1            0            103
  R2            0              5
  RX            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, continuous
D18V8, continuous
D18V9, continuous
D18V10, continuous
D18V11, continuous
D18V12, continuous
D18V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPTN MUTATED       0                         1     2
  RPTN WILD-TYPE     2                         6   145
D18V14, multiclass
                           clus
vv                          RPTN MUTATED RPTN WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                                2            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = TCEB3 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  TCEB3 MUTATED     4   0
  TCEB3 WILD-TYPE 408   7
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              4             415 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              0               7 
$`TCEB3 MUTATED`
TCGA-CH-5766 TCGA-EJ-5530 TCGA-J9-A52B TCGA-J9-A52C 
        1.02        60.23        13.87         5.85 

$`TCEB3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00         1.02        23.01        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       38.76        39.75        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       14.37        20.28         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  TCEB3 MUTATED TCEB3 WILD-TYPE 
           1.02            0.72 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
          60.23          165.17 
  TCEB3 MUTATED TCEB3 WILD-TYPE 
           9.86           27.39 
[1] "1.0 - 60.2 (9.9)"   "0.7 - 165.2 (27.4)"
[1] "hr="     "3300000"
D19V2, continuous
                 vv
clus               T2  T3  T4
  TCEB3 MUTATED     1   3   0
  TCEB3 WILD-TYPE 171 236   6
D19V3, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  T2             1             171
  T3             3             236
  T4             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"
D19V4, binary
                 cls
clus                0   1
  TCEB3 MUTATED     2   1
  TCEB3 WILD-TYPE 297  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      2    1
  TCEB3 WILD-TYPE  297   57
   clus
vv  TCEB3 MUTATED TCEB3 WILD-TYPE
  0             2             297
  1             1              57
[1] 2 2
[1] FALSE
D19V5, binary
                 cls
clus                0   1
  TCEB3 MUTATED     0   4
  TCEB3 WILD-TYPE  15 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TCEB3 MUTATED      0    4
  TCEB3 WILD-TYPE   15  401
                                        clus
vv                                       TCEB3 MUTATED TCEB3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             401
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  TCEB3 MUTATED     3   1   0   0
  TCEB3 WILD-TYPE 280 102   5  15
D19V6, multiclass
    clus
vv   TCEB3 MUTATED TCEB3 WILD-TYPE
  R0             3             280
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, continuous
D19V8, continuous
D19V9, continuous
D19V10, continuous
D19V11, continuous
D19V12, continuous
D19V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCEB3 MUTATED       0                         0     2
  TCEB3 WILD-TYPE     2                         7   145
D19V14, multiclass
[1] "Remove cluster labels:" "TCEB3 MUTATED"         
clus
  TCEB3 MUTATED TCEB3 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"TCEB3 WILD-TYPE" "TCEB3 WILD-TYPE" 

Clustering(20) Variable = NTM MUTATION ANALYSIS
D20V1, survival
               sevent
clus2             0   1
  NTM MUTATED     5   0
  NTM WILD-TYPE 407   7
  NTM MUTATED NTM WILD-TYPE 
            5           414 
  NTM MUTATED NTM WILD-TYPE 
            0             7 
$`NTM MUTATED`
TCGA-EJ-5531 TCGA-G9-6356 TCGA-G9-6362 TCGA-HC-7213 TCGA-HC-7748 
       41.85        47.15        47.44        40.08        26.04 

$`NTM WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        39.75        60.23        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       46.16        50.70        49.35        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54         0.79        28.60         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7749 TCGA-HC-7750 
        1.48         1.68        23.70        24.59         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  NTM MUTATED NTM WILD-TYPE 
        26.04          0.72 
  NTM MUTATED NTM WILD-TYPE 
        47.44        165.17 
  NTM MUTATED NTM WILD-TYPE 
       41.850        27.175 
[1] "26.0 - 47.4 (41.9)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9200000"
D20V2, continuous
               vv
clus             T2  T3  T4
  NTM MUTATED     1   4   0
  NTM WILD-TYPE 171 235   6
D20V3, multiclass
    clus
vv   NTM MUTATED NTM WILD-TYPE
  T2           1           171
  T3           4           235
  T4           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"
D20V4, binary
               cls
clus              0   1
  NTM MUTATED     5   0
  NTM WILD-TYPE 294  58
[1] "tbl2"
               cls
clus            [,1] [,2]
  NTM MUTATED      5    0
  NTM WILD-TYPE  294   58
   clus
vv  NTM MUTATED NTM WILD-TYPE
  0           5           294
  1           0            58
[1] 2 2
[1] FALSE
D20V5, binary
               cls
clus              0   1
  NTM MUTATED     0   5
  NTM WILD-TYPE  15 400
[1] "tbl2"
               cls
clus            [,1] [,2]
  NTM MUTATED      0    5
  NTM WILD-TYPE   15  400
                                        clus
vv                                       NTM MUTATED NTM WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE           0            15
  PROSTATE ADENOCARCINOMA ACINAR TYPE              5           400
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  NTM MUTATED     3   2   0   0
  NTM WILD-TYPE 280 101   5  15
D20V6, multiclass
    clus
vv   NTM MUTATED NTM WILD-TYPE
  R0           3           280
  R1           2           101
  R2           0             5
  RX           0            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, continuous
D20V8, continuous
D20V9, continuous
D20V10, continuous
D20V11, continuous
D20V12, continuous
D20V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NTM MUTATED       0                         0     5
  NTM WILD-TYPE     2                         7   142
D20V14, multiclass
                           clus
vv                          NTM MUTATED NTM WILD-TYPE
  ASIAN                               0             2
  BLACK OR AFRICAN AMERICAN           0             7
  WHITE                               5           142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = MED12 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  MED12 MUTATED     7   0
  MED12 WILD-TYPE 405   7
  MED12 MUTATED MED12 WILD-TYPE 
              7             412 
  MED12 MUTATED MED12 WILD-TYPE 
              0               7 
$`MED12 MUTATED`
TCGA-CH-5748 TCGA-EJ-5510 TCGA-G9-6362 TCGA-G9-7519 TCGA-HC-A6AL TCGA-KC-A7F3 
        1.02        36.69        47.44        27.91         2.20        21.86 
TCGA-VP-A87J 
       53.36 

$`MED12 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97         2.99        24.03        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5511 
       30.31        27.19        23.90        38.93        48.13        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 
       50.70        49.35        47.15        46.52        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7521 
       58.22        56.75        64.18        50.73        38.96        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AN 
        1.15        22.36         0.76         1.78         2.01         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V 
        2.99         8.65        19.66         8.88        11.57       113.10 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87K 
       85.18        55.56        60.92        66.97        21.80        42.94 
TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G 
       14.76        45.47        32.19         3.91        37.05        38.04 
TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL 
       42.08        48.03         9.04         2.99        31.99        25.48 
TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO 
        4.87        52.96        49.02        51.45        48.72        71.77 
TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF 
       62.14        60.56        16.83        56.52        41.46        45.14 
TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP 
       28.77        45.86        46.29        32.45       114.38        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       62.79         8.98        14.04        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  MED12 MUTATED MED12 WILD-TYPE 
           1.02            0.72 
  MED12 MUTATED MED12 WILD-TYPE 
          53.36          165.17 
  MED12 MUTATED MED12 WILD-TYPE 
          27.91           27.24 
[1] "1.0 - 53.4 (27.9)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D21V2, continuous
                 vv
clus               T2  T3  T4
  MED12 MUTATED     4   3   0
  MED12 WILD-TYPE 168 236   6
D21V3, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  T2             4             168
  T3             3             236
  T4             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"
D21V4, binary
                 cls
clus                0   1
  MED12 MUTATED     5   1
  MED12 WILD-TYPE 294  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      5    1
  MED12 WILD-TYPE  294   57
   clus
vv  MED12 MUTATED MED12 WILD-TYPE
  0             5             294
  1             1              57
[1] 2 2
[1] FALSE
D21V5, binary
                 cls
clus                0   1
  MED12 MUTATED     0   7
  MED12 WILD-TYPE  15 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED12 MUTATED      0    7
  MED12 WILD-TYPE   15  398
                                        clus
vv                                       MED12 MUTATED MED12 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             398
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED12 MUTATED     4   2   1   0
  MED12 WILD-TYPE 279 101   4  15
D21V6, multiclass
    clus
vv   MED12 MUTATED MED12 WILD-TYPE
  R0             4             279
  R1             2             101
  R2             1               4
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, continuous
D21V8, continuous
D21V9, continuous
D21V10, continuous
D21V11, continuous
D21V12, continuous
D21V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED12 MUTATED       0                         0     3
  MED12 WILD-TYPE     2                         7   144
D21V14, multiclass
                           clus
vv                          MED12 MUTATED MED12 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = MED15 MUTATION ANALYSIS
D22V1, survival
                 sevent
clus2               0   1
  MED15 MUTATED     6   0
  MED15 WILD-TYPE 406   7
  MED15 MUTATED MED15 WILD-TYPE 
              6             413 
  MED15 MUTATED MED15 WILD-TYPE 
              0               7 
$`MED15 MUTATED`
TCGA-CH-5764 TCGA-EJ-7782 TCGA-G9-7523 TCGA-HC-7211 TCGA-J4-A83M TCGA-KK-A59V 
        1.02        38.37        28.18         0.79        14.37       113.10 

$`MED15 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 
       27.68         6.28        24.39        23.90        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       27.91        30.97        35.34        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       14.47        28.54        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83N TCGA-J9-A52B 
       22.52        22.88        10.78        23.67        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37         3.09        14.53        13.28        10.13 

  MED15 MUTATED MED15 WILD-TYPE 
           0.79            0.72 
  MED15 MUTATED MED15 WILD-TYPE 
         113.10          165.17 
  MED15 MUTATED MED15 WILD-TYPE 
         21.275          27.290 
[1] "0.8 - 113.1 (21.3)" "0.7 - 165.2 (27.3)"
[1] "hr="     "9100000"
D22V2, continuous
                 vv
clus               T2  T3  T4
  MED15 MUTATED     3   3   0
  MED15 WILD-TYPE 169 236   6
D22V3, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  T2             3             169
  T3             3             236
  T4             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"
D22V4, binary
                 cls
clus                0   1
  MED15 MUTATED     6   0
  MED15 WILD-TYPE 293  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      6    0
  MED15 WILD-TYPE  293   58
   clus
vv  MED15 MUTATED MED15 WILD-TYPE
  0             6             293
  1             0              58
[1] 2 2
[1] FALSE
D22V5, binary
                 cls
clus                0   1
  MED15 MUTATED     0   6
  MED15 WILD-TYPE  15 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MED15 MUTATED      0    6
  MED15 WILD-TYPE   15  399
                                        clus
vv                                       MED15 MUTATED MED15 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             399
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MED15 MUTATED     4   2   0   0
  MED15 WILD-TYPE 279 101   5  15
D22V6, multiclass
    clus
vv   MED15 MUTATED MED15 WILD-TYPE
  R0             4             279
  R1             2             101
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, continuous
D22V8, continuous
D22V9, continuous
D22V10, continuous
D22V11, continuous
D22V12, continuous
D22V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MED15 MUTATED       0                         1     2
  MED15 WILD-TYPE     2                         6   145
D22V14, multiclass
                           clus
vv                          MED15 MUTATED MED15 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 2             145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = ERN1 MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  ERN1 MUTATED     3   0
  ERN1 WILD-TYPE 409   7
  ERN1 MUTATED ERN1 WILD-TYPE 
             3            416 
  ERN1 MUTATED ERN1 WILD-TYPE 
             0              7 
$`ERN1 MUTATED`
TCGA-J4-A83J TCGA-KK-A7AQ TCGA-V1-A8MU 
       22.88        52.93        53.16 

$`ERN1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       32.68         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K 
        6.02        25.28        27.91        16.83        22.52        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       23.67        14.37        20.28        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        86.40        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       58.19         6.44        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        39.29        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  ERN1 MUTATED ERN1 WILD-TYPE 
         22.88           0.72 
  ERN1 MUTATED ERN1 WILD-TYPE 
         53.16         165.17 
  ERN1 MUTATED ERN1 WILD-TYPE 
         52.93          27.24 
[1] "22.9 - 53.2 (52.9)" "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D23V2, continuous
                vv
clus              T2  T3  T4
  ERN1 MUTATED     2   1   0
  ERN1 WILD-TYPE 170 238   6
D23V3, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  T2            2            170
  T3            1            238
  T4            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"
D23V4, binary
                cls
clus               0   1
  ERN1 MUTATED     2   1
  ERN1 WILD-TYPE 297  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      2    1
  ERN1 WILD-TYPE  297   57
   clus
vv  ERN1 MUTATED ERN1 WILD-TYPE
  0            2            297
  1            1             57
[1] 2 2
[1] FALSE
D23V5, binary
                cls
clus               0   1
  ERN1 MUTATED     0   3
  ERN1 WILD-TYPE  15 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  ERN1 MUTATED      0    3
  ERN1 WILD-TYPE   15  402
                                        clus
vv                                       ERN1 MUTATED ERN1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ERN1 MUTATED     1   2   0   0
  ERN1 WILD-TYPE 282 101   5  15
D23V6, multiclass
    clus
vv   ERN1 MUTATED ERN1 WILD-TYPE
  R0            1            282
  R1            2            101
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, continuous
D23V8, continuous
D23V9, continuous
D23V10, continuous
D23V11, continuous
D23V12, continuous
D23V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERN1 MUTATED       0                         0     0
  ERN1 WILD-TYPE     2                         7   147
D23V14, multiclass

Clustering(24) Variable = LMOD2 MUTATION ANALYSIS
D24V1, survival
                 sevent
clus2               0   1
  LMOD2 MUTATED     5   0
  LMOD2 WILD-TYPE 407   7
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              5             414 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              0               7 
$`LMOD2 MUTATED`
TCGA-EJ-A46B TCGA-EJ-A8FN TCGA-HC-7212 TCGA-J4-A67Q TCGA-J9-A8CM 
       21.60        10.82        28.60        32.05        15.22 

$`LMOD2 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46D TCGA-EJ-A46E 
       76.41        38.10        24.85        25.18        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21         6.48         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 TCGA-HC-7230 
       37.35        14.47        28.54         0.79        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CN 
       13.87         5.85         6.97        10.62        13.32        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  LMOD2 MUTATED LMOD2 WILD-TYPE 
          10.82            0.72 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
          32.05          165.17 
  LMOD2 MUTATED LMOD2 WILD-TYPE 
          21.60           27.34 
[1] "10.8 - 32.0 (21.6)" "0.7 - 165.2 (27.3)"
[1] "hr="     "3300000"
D24V2, continuous
                 vv
clus               T2  T3  T4
  LMOD2 MUTATED     3   2   0
  LMOD2 WILD-TYPE 169 237   6
D24V3, multiclass
    clus
vv   LMOD2 MUTATED LMOD2 WILD-TYPE
  T2             3             169
  T3             2             237
  T4             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"
D24V4, binary
                 cls
clus                0   1
  LMOD2 MUTATED     3   1
  LMOD2 WILD-TYPE 296  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      3    1
  LMOD2 WILD-TYPE  296   57
   clus
vv  LMOD2 MUTATED LMOD2 WILD-TYPE
  0             3             296
  1             1              57
[1] 2 2
[1] FALSE
D24V5, binary
                 cls
clus                0   1
  LMOD2 MUTATED     0   5
  LMOD2 WILD-TYPE  15 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LMOD2 MUTATED      0    5
  LMOD2 WILD-TYPE   15  400
                                        clus
vv                                       LMOD2 MUTATED LMOD2 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             400
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LMOD2 MUTATED     2   1   0   0
  LMOD2 WILD-TYPE 281 102   5  15
D24V6, multiclass
    clus
vv   LMOD2 MUTATED LMOD2 WILD-TYPE
  R0             2             281
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, continuous
D24V8, continuous
D24V9, continuous
D24V10, continuous
D24V11, continuous
D24V12, continuous
D24V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LMOD2 MUTATED       0                         0     1
  LMOD2 WILD-TYPE     2                         7   146
D24V14, multiclass
[1] "Remove cluster labels:" "LMOD2 MUTATED"         
clus
  LMOD2 MUTATED LMOD2 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7210      TCGA-HC-7211      TCGA-HC-7213      TCGA-HC-7230 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" "LMOD2 WILD-TYPE" 

Clustering(25) Variable = FAM111A MUTATION ANALYSIS
D25V1, survival
                   sevent
clus2                 0   1
  FAM111A MUTATED     2   1
  FAM111A WILD-TYPE 410   6
  FAM111A MUTATED FAM111A WILD-TYPE 
                3               416 
  FAM111A MUTATED FAM111A WILD-TYPE 
                1                 6 
$`FAM111A MUTATED`
TCGA-EJ-5519 TCGA-J4-A67N TCGA-KK-A8II 
       64.50        16.54       113.98 

$`FAM111A WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       47.80        52.27        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
       66.18        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  FAM111A MUTATED FAM111A WILD-TYPE 
            16.54              0.72 
  FAM111A MUTATED FAM111A WILD-TYPE 
           113.98            165.17 
  FAM111A MUTATED FAM111A WILD-TYPE 
            64.50             27.24 
[1] "16.5 - 114.0 (64.5)" "0.7 - 165.2 (27.2)" 
[1] "hr=" "6.6"
D25V2, continuous
                   vv
clus                 T2  T3  T4
  FAM111A MUTATED     0   3   0
  FAM111A WILD-TYPE 172 236   6
D25V3, multiclass
    clus
vv   FAM111A MUTATED FAM111A WILD-TYPE
  T2               0               172
  T3               3               236
  T4               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"
D25V4, binary
                   cls
clus                  0   1
  FAM111A MUTATED     2   1
  FAM111A WILD-TYPE 297  57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED      2    1
  FAM111A WILD-TYPE  297   57
   clus
vv  FAM111A MUTATED FAM111A WILD-TYPE
  0               2               297
  1               1                57
[1] 2 2
[1] FALSE
D25V5, binary
                   cls
clus                  0   1
  FAM111A MUTATED     1   2
  FAM111A WILD-TYPE  14 403
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM111A MUTATED      1    2
  FAM111A WILD-TYPE   14  403
                                        clus
vv                                       FAM111A MUTATED FAM111A WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               1                14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  2               403
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM111A MUTATED     3   0   0   0
  FAM111A WILD-TYPE 280 103   5  15
D25V6, multiclass
    clus
vv   FAM111A MUTATED FAM111A WILD-TYPE
  R0               3               280
  R1               0               103
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, continuous
[1] "Remove cluster labels:" "FAM111A MUTATED"       
clus
  FAM111A MUTATED FAM111A WILD-TYPE 
                2               340 
       TCGA-2A-A8VL        TCGA-2A-A8VT        TCGA-2A-A8VV        TCGA-2A-A8VX 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-2A-A8W1        TCGA-2A-A8W3        TCGA-CH-5737        TCGA-CH-5739 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5745        TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7218        TCGA-EJ-7312        TCGA-EJ-7314 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7325 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7794        TCGA-EJ-7797 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8472 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-8474        TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A46F        TCGA-EJ-A46G        TCGA-EJ-A65B        TCGA-EJ-A65D 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A65E        TCGA-EJ-A65F        TCGA-EJ-A65G        TCGA-EJ-A65J 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A65M        TCGA-EJ-A6RA        TCGA-EJ-A6RC        TCGA-EJ-A7NF 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A7NG        TCGA-EJ-A7NJ        TCGA-EJ-A7NK        TCGA-EJ-A7NM 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A7NN        TCGA-EJ-A8FN        TCGA-EJ-A8FO        TCGA-EJ-A8FP 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-A8FS        TCGA-EJ-A8FU        TCGA-FC-7708        TCGA-FC-7961 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-FC-A66V        TCGA-FC-A6HD        TCGA-FC-A8O0 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6339        TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6361 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6362        TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6377 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6379        TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-7523        TCGA-G9-7525        TCGA-H9-A6BY        TCGA-HC-7078 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7209        TCGA-HC-7210 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7233        TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7740 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7742        TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7748        TCGA-HC-7749        TCGA-HC-7752        TCGA-HC-7818 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7821        TCGA-HC-8216        TCGA-HC-8257 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-8258        TCGA-HC-8260        TCGA-HC-8262        TCGA-HC-8264 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-8265        TCGA-HC-8266        TCGA-HC-A48F        TCGA-HC-A4ZV 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-A631        TCGA-HC-A632        TCGA-HC-A6AL        TCGA-HC-A6AN 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-A6AS        TCGA-HC-A6HX        TCGA-HC-A76W        TCGA-HC-A76X 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-A8CY        TCGA-HC-A8D0        TCGA-HC-A8D1        TCGA-HI-7168 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8200 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-J4-A67L        TCGA-J4-A67M        TCGA-J4-A67O        TCGA-J4-A67R 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-J4-A67S        TCGA-J4-A6G1        TCGA-J4-A6G3        TCGA-J4-A83I 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-J4-A83J        TCGA-J4-A83L        TCGA-J4-A83M        TCGA-J9-A52B 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-J9-A52E        TCGA-J9-A8CM        TCGA-KC-A4BL        TCGA-KC-A4BN 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KC-A4BO        TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KC-A7F3 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KC-A7F5        TCGA-KC-A7F6        TCGA-KC-A7FA        TCGA-KC-A7FD 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KC-A7FE        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1        TCGA-KK-A6DY        TCGA-KK-A6E0 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A6E1        TCGA-KK-A6E2        TCGA-KK-A6E3        TCGA-KK-A6E4 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A6E5        TCGA-KK-A6E6        TCGA-KK-A6E7        TCGA-KK-A6E8 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A7AP        TCGA-KK-A7AQ        TCGA-KK-A7AU        TCGA-KK-A7AV 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A7AW        TCGA-KK-A7AY        TCGA-KK-A7AZ        TCGA-KK-A7B0 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A7B1        TCGA-KK-A7B2        TCGA-KK-A7B3        TCGA-KK-A7B4 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A8I4        TCGA-KK-A8I6        TCGA-KK-A8I7        TCGA-KK-A8IA 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-KK-A8ID        TCGA-KK-A8IJ        TCGA-KK-A8IL        TCGA-M7-A71Z 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-M7-A722        TCGA-M7-A723        TCGA-M7-A724        TCGA-M7-A725 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-QU-A6IL        TCGA-QU-A6IM        TCGA-QU-A6IN        TCGA-QU-A6IO 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-QU-A6IP        TCGA-SU-A7E7        TCGA-V1-A8MF        TCGA-V1-A8MJ 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-V1-A8ML        TCGA-V1-A8MM        TCGA-V1-A8MU        TCGA-V1-A8WL 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-V1-A8WV        TCGA-V1-A8X3        TCGA-VN-A88I        TCGA-VN-A88K 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VN-A88L        TCGA-VN-A88M        TCGA-VN-A88N        TCGA-VN-A88O 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VN-A88P        TCGA-VN-A88Q        TCGA-VN-A88R        TCGA-VP-A872 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VP-A875        TCGA-VP-A876        TCGA-VP-A878        TCGA-VP-A879 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VP-A87B        TCGA-VP-A87C        TCGA-VP-A87D        TCGA-VP-A87E 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-VP-A87H        TCGA-VP-A87J        TCGA-VP-A87K        TCGA-WW-A8ZI 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-X4-A8KQ        TCGA-XA-A8JR        TCGA-XJ-A83F        TCGA-XJ-A83G 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-XJ-A9DI        TCGA-XJ-A9DX        TCGA-Y6-A8TL        TCGA-YJ-A8SW 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-YL-A8HK        TCGA-YL-A8HL        TCGA-YL-A8HM        TCGA-YL-A8HO 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-YL-A8S8        TCGA-YL-A8S9        TCGA-YL-A8SA        TCGA-YL-A8SB 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-YL-A8SC        TCGA-YL-A8SF        TCGA-YL-A8SH        TCGA-YL-A8SJ 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-YL-A8SK        TCGA-YL-A8SL        TCGA-YL-A8SQ        TCGA-YL-A8SR 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-YL-A9WH        TCGA-YL-A9WI        TCGA-YL-A9WJ        TCGA-YL-A9WK 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-ZG-A8QW        TCGA-ZG-A8QX        TCGA-ZG-A8QY        TCGA-ZG-A8QZ 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
D25V8, continuous
D25V9, continuous
D25V10, continuous
D25V11, continuous
D25V12, continuous
D25V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM111A MUTATED       0                         0     1
  FAM111A WILD-TYPE     2                         7   146
D25V14, multiclass
[1] "Remove cluster labels:" "FAM111A MUTATED"       
clus
  FAM111A MUTATED FAM111A WILD-TYPE 
                1               155 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5521        TCGA-EJ-5522 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"FAM111A WILD-TYPE" "FAM111A WILD-TYPE" "FAM111A WILD-TYPE" 

Clustering(26) Variable = ZNF709 MUTATION ANALYSIS
D26V1, survival
                  sevent
clus2                0   1
  ZNF709 MUTATED     5   0
  ZNF709 WILD-TYPE 407   7
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               5              414 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               0                7 
$`ZNF709 MUTATED`
TCGA-EJ-7328 TCGA-EJ-8469 TCGA-HC-7744 TCGA-KK-A59V TCGA-XJ-A9DI 
       27.68        76.41         1.68       113.10        48.03 

$`ZNF709 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8470 
       17.29         3.75        23.05        19.92        77.16        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       31.69        23.57         1.48        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DK TCGA-XJ-A9DQ 
        3.91        37.05        38.04        42.08         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  ZNF709 MUTATED ZNF709 WILD-TYPE 
            1.68             0.72 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
          113.10           165.17 
  ZNF709 MUTATED ZNF709 WILD-TYPE 
          48.030           27.175 
[1] "1.7 - 113.1 (48.0)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9300000"
D26V2, continuous
                  vv
clus                T2  T3  T4
  ZNF709 MUTATED     0   5   0
  ZNF709 WILD-TYPE 172 234   6
D26V3, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  T2              0              172
  T3              5              234
  T4              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"
D26V4, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     5   0
  ZNF709 WILD-TYPE 294  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      5    0
  ZNF709 WILD-TYPE  294   58
   clus
vv  ZNF709 MUTATED ZNF709 WILD-TYPE
  0              5              294
  1              0               58
[1] 2 2
[1] FALSE
D26V5, binary
                  cls
clus                 0   1
  ZNF709 MUTATED     0   5
  ZNF709 WILD-TYPE  15 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF709 MUTATED      0    5
  ZNF709 WILD-TYPE   15  400
                                        clus
vv                                       ZNF709 MUTATED ZNF709 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              400
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ZNF709 MUTATED     3   1   0   1
  ZNF709 WILD-TYPE 280 102   5  14
D26V6, multiclass
    clus
vv   ZNF709 MUTATED ZNF709 WILD-TYPE
  R0              3              280
  R1              1              102
  R2              0                5
  RX              1               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, continuous
D26V8, continuous
D26V9, continuous
D26V10, continuous
D26V11, continuous
D26V12, continuous
D26V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF709 MUTATED       0                         0     2
  ZNF709 WILD-TYPE     2                         7   145
D26V14, multiclass
[1] "Remove cluster labels:" "ZNF709 MUTATED"        
clus
  ZNF709 MUTATED ZNF709 WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7330       TCGA-EJ-7331       TCGA-EJ-7781 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"ZNF709 WILD-TYPE" "ZNF709 WILD-TYPE" 

Clustering(27) Variable = MLLT10 MUTATION ANALYSIS
D27V1, survival
                  sevent
clus2                0   1
  MLLT10 MUTATED     4   0
  MLLT10 WILD-TYPE 408   7
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               4              415 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
               0                7 
$`MLLT10 MUTATED`
TCGA-CH-5761 TCGA-EJ-5498 TCGA-EJ-5505 TCGA-EJ-5516 
        0.92        29.79        30.31        46.55 

$`MLLT10 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 
       35.01        31.00         1.02         2.04        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5506 
       46.52        44.88        26.30        45.73        28.93        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       36.23        60.23        47.80        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       68.35        43.07        36.66        38.76        39.75        60.23 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.85        47.87        29.06        88.34        74.10        93.70 
TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 
       83.57        36.13        37.81        33.14        25.35        33.83 
TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       27.09        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
       23.90        38.37        25.87        25.68        20.55        14.53 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 
       14.14        18.15        19.59        17.29         3.75        23.05 
TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 
       19.92        77.16        76.41        38.10        24.85        25.18 
TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H 
       21.60        20.58        17.23        25.74        21.96        23.80 
TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G 
       21.96        23.34        12.92        13.71        18.41        21.90 
TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       14.83         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN 
       15.58         6.48        15.65         4.21         6.48        10.82 
TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 
        9.27         9.83         8.75         4.54        28.41        15.42 
TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 
       13.45        22.36        17.23        16.24         1.78        41.62 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 
       87.35        81.04        67.99        66.67        83.87        55.76 
TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 
       18.21        68.68        49.81        46.16        50.70        49.35 
TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 
       47.15        46.52        47.44        45.30        39.39        44.81 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        40.18        39.95        38.01        40.31        26.66 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       31.50        37.97        58.45        25.15        27.29        58.22 
TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 
       56.75        64.18        50.73        38.96        27.91        30.97 
TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY 
       35.34        28.18        32.68         6.08        30.94         3.68 
TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 
       19.76        65.26         2.93        36.36        37.35        14.47 
TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 
       28.54         0.79        28.60        40.08         1.68         2.37 
TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 
       38.17        44.55         0.72         2.10        31.69        23.57 
TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
        1.48         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  MLLT10 MUTATED MLLT10 WILD-TYPE 
            0.92             0.72 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           46.55           165.17 
  MLLT10 MUTATED MLLT10 WILD-TYPE 
           30.05            27.19 
[1] "0.9 - 46.5 (30.0)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D27V2, continuous
                  vv
clus                T2  T3  T4
  MLLT10 MUTATED     2   2   0
  MLLT10 WILD-TYPE 170 237   6
D27V3, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  T2              2              170
  T3              2              237
  T4              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"
D27V4, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     4   0
  MLLT10 WILD-TYPE 295  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      4    0
  MLLT10 WILD-TYPE  295   58
   clus
vv  MLLT10 MUTATED MLLT10 WILD-TYPE
  0              4              295
  1              0               58
[1] 2 2
[1] FALSE
D27V5, binary
                  cls
clus                 0   1
  MLLT10 MUTATED     0   4
  MLLT10 WILD-TYPE  15 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  MLLT10 MUTATED      0    4
  MLLT10 WILD-TYPE   15  401
                                        clus
vv                                       MLLT10 MUTATED MLLT10 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              401
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  MLLT10 MUTATED     4   0   0   0
  MLLT10 WILD-TYPE 279 103   5  15
D27V6, multiclass
    clus
vv   MLLT10 MUTATED MLLT10 WILD-TYPE
  R0              4              279
  R1              0              103
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, continuous
D27V8, continuous
D27V9, continuous
D27V10, continuous
D27V11, continuous
D27V12, continuous
D27V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLLT10 MUTATED       0                         0     4
  MLLT10 WILD-TYPE     2                         7   143
D27V14, multiclass
                           clus
vv                          MLLT10 MUTATED MLLT10 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  4              143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = TNRC18 MUTATION ANALYSIS
D28V1, survival
                  sevent
clus2                0   1
  TNRC18 MUTATED     4   0
  TNRC18 WILD-TYPE 408   7
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               4              415 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               0                7 
$`TNRC18 MUTATED`
TCGA-EJ-7330 TCGA-HC-7742 TCGA-KK-A6E1 TCGA-QU-A6IN 
        6.28         1.48        54.54       140.19 

$`TNRC18 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35        27.68        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
        2.10        31.69        23.57         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E2 TCGA-KK-A6E3 
       86.40        77.72       115.86        30.02       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
       18.84         3.19        41.00       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  TNRC18 MUTATED TNRC18 WILD-TYPE 
            1.48             0.72 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
          140.19           165.17 
  TNRC18 MUTATED TNRC18 WILD-TYPE 
           30.41            27.29 
[1] "1.5 - 140.2 (30.4)" "0.7 - 165.2 (27.3)"
[1] "hr="     "3.2e+07"
D28V2, continuous
                  vv
clus                T2  T3  T4
  TNRC18 MUTATED     1   3   0
  TNRC18 WILD-TYPE 171 236   6
D28V3, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  T2              1              171
  T3              3              236
  T4              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"
D28V4, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     3   1
  TNRC18 WILD-TYPE 296  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      3    1
  TNRC18 WILD-TYPE  296   57
   clus
vv  TNRC18 MUTATED TNRC18 WILD-TYPE
  0              3              296
  1              1               57
[1] 2 2
[1] FALSE
D28V5, binary
                  cls
clus                 0   1
  TNRC18 MUTATED     0   4
  TNRC18 WILD-TYPE  15 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TNRC18 MUTATED      0    4
  TNRC18 WILD-TYPE   15  401
                                        clus
vv                                       TNRC18 MUTATED TNRC18 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              401
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TNRC18 MUTATED     3   0   0   1
  TNRC18 WILD-TYPE 280 103   5  14
D28V6, multiclass
    clus
vv   TNRC18 MUTATED TNRC18 WILD-TYPE
  R0              3              280
  R1              0              103
  R2              0                5
  RX              1               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, continuous
D28V8, continuous
D28V9, continuous
D28V10, continuous
D28V11, continuous
D28V12, continuous
D28V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TNRC18 MUTATED       0                         0     2
  TNRC18 WILD-TYPE     2                         7   145
D28V14, multiclass
[1] "Remove cluster labels:" "TNRC18 MUTATED"        
clus
  TNRC18 MUTATED TNRC18 WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7331       TCGA-EJ-7781 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7744 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"TNRC18 WILD-TYPE" "TNRC18 WILD-TYPE" 

Clustering(29) Variable = GAGE2D MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2                0   1
  GAGE2D MUTATED     3   0
  GAGE2D WILD-TYPE 409   7
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               3              416 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               0                7 
$`GAGE2D MUTATED`
TCGA-EJ-5497 TCGA-G9-6348 TCGA-M7-A720 
       13.32        49.81        12.62 

$`GAGE2D WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6351 
       66.67        83.87        55.76        18.21        68.68        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
        5.19        21.14        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  GAGE2D MUTATED GAGE2D WILD-TYPE 
           12.62             0.72 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           49.81           165.17 
  GAGE2D MUTATED GAGE2D WILD-TYPE 
           13.32            27.34 
[1] "12.6 - 49.8 (13.3)" "0.7 - 165.2 (27.3)"
[1] "hr="     "3300000"
D29V2, continuous
                  vv
clus                T2  T3  T4
  GAGE2D MUTATED     3   0   0
  GAGE2D WILD-TYPE 169 239   6
D29V3, multiclass
    clus
vv   GAGE2D MUTATED GAGE2D WILD-TYPE
  T2              3              169
  T3              0              239
  T4              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"
D29V4, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     2   0
  GAGE2D WILD-TYPE 297  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      2    0
  GAGE2D WILD-TYPE  297   58
   clus
vv  GAGE2D MUTATED GAGE2D WILD-TYPE
  0              2              297
  1              0               58
[1] 2 2
[1] FALSE
D29V5, binary
                  cls
clus                 0   1
  GAGE2D MUTATED     0   3
  GAGE2D WILD-TYPE  15 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  GAGE2D MUTATED      0    3
  GAGE2D WILD-TYPE   15  402
                                        clus
vv                                       GAGE2D MUTATED GAGE2D WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 3              402
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  GAGE2D MUTATED     3   0   0   0
  GAGE2D WILD-TYPE 280 103   5  15
D29V6, multiclass
    clus
vv   GAGE2D MUTATED GAGE2D WILD-TYPE
  R0              3              280
  R1              0              103
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, continuous
[1] "Remove cluster labels:" "GAGE2D MUTATED"        
clus
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               2              340 
      TCGA-2A-A8VL       TCGA-2A-A8VT       TCGA-2A-A8VV       TCGA-2A-A8VX 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-2A-A8W1       TCGA-2A-A8W3       TCGA-CH-5737       TCGA-CH-5739 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5740       TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5745       TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5761       TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5789       TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5794       TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5502 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5503       TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5507       TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5511       TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5516       TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5521       TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5526       TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5532       TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7125       TCGA-EJ-7218       TCGA-EJ-7312       TCGA-EJ-7314 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7325 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7794       TCGA-EJ-7797 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-8468       TCGA-EJ-8469       TCGA-EJ-8470       TCGA-EJ-8472 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-8474       TCGA-EJ-A46B       TCGA-EJ-A46D       TCGA-EJ-A46E 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A46F       TCGA-EJ-A46G       TCGA-EJ-A65B       TCGA-EJ-A65D 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A65E       TCGA-EJ-A65F       TCGA-EJ-A65G       TCGA-EJ-A65J 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A65M       TCGA-EJ-A6RA       TCGA-EJ-A6RC       TCGA-EJ-A7NF 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A7NG       TCGA-EJ-A7NJ       TCGA-EJ-A7NK       TCGA-EJ-A7NM 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A7NN       TCGA-EJ-A8FN       TCGA-EJ-A8FO       TCGA-EJ-A8FP 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A8FS       TCGA-EJ-A8FU       TCGA-FC-7708       TCGA-FC-7961 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FC-A5OB       TCGA-FC-A66V       TCGA-FC-A6HD       TCGA-FC-A8O0 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6339       TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6363       TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6367 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6377       TCGA-G9-6379 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6384       TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-7510       TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-7525       TCGA-H9-A6BY       TCGA-HC-7078       TCGA-HC-7079 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7233 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7736       TCGA-HC-7737       TCGA-HC-7740       TCGA-HC-7742 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7821       TCGA-HC-8216       TCGA-HC-8257       TCGA-HC-8258 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-8260       TCGA-HC-8262       TCGA-HC-8264       TCGA-HC-8265 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-8266       TCGA-HC-A48F       TCGA-HC-A4ZV       TCGA-HC-A631 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-A632       TCGA-HC-A6AL       TCGA-HC-A6AN       TCGA-HC-A6AS 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-A6HX       TCGA-HC-A76W       TCGA-HC-A76X       TCGA-HC-A8CY 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-A8D0       TCGA-HC-A8D1       TCGA-HI-7168       TCGA-HI-7169 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171       TCGA-J4-8200       TCGA-J4-A67L 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A67M       TCGA-J4-A67N       TCGA-J4-A67O       TCGA-J4-A67R 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A67S       TCGA-J4-A6G1       TCGA-J4-A6G3       TCGA-J4-A83I 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A83J       TCGA-J4-A83L       TCGA-J4-A83M       TCGA-J9-A52B 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J9-A52E       TCGA-J9-A8CM       TCGA-KC-A4BL       TCGA-KC-A4BN 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A4BO       TCGA-KC-A4BR       TCGA-KC-A4BV       TCGA-KC-A7F3 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A7F5       TCGA-KC-A7F6       TCGA-KC-A7FA       TCGA-KC-A7FD 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A7FE       TCGA-KK-A59V       TCGA-KK-A59X       TCGA-KK-A59Y 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A59Z       TCGA-KK-A5A1       TCGA-KK-A6DY       TCGA-KK-A6E0 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A6E1       TCGA-KK-A6E2       TCGA-KK-A6E3       TCGA-KK-A6E4 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A6E5       TCGA-KK-A6E6       TCGA-KK-A6E7       TCGA-KK-A6E8 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7AP       TCGA-KK-A7AQ       TCGA-KK-A7AU       TCGA-KK-A7AV 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7AW       TCGA-KK-A7AY       TCGA-KK-A7AZ       TCGA-KK-A7B0 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7B1       TCGA-KK-A7B2       TCGA-KK-A7B3       TCGA-KK-A7B4 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8I4       TCGA-KK-A8I6       TCGA-KK-A8I7       TCGA-KK-A8IA 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8ID       TCGA-KK-A8IJ       TCGA-KK-A8IL       TCGA-M7-A71Z 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-M7-A722       TCGA-M7-A723       TCGA-M7-A724       TCGA-M7-A725 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QU-A6IL       TCGA-QU-A6IM       TCGA-QU-A6IN       TCGA-QU-A6IO 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QU-A6IP       TCGA-SU-A7E7       TCGA-V1-A8MF       TCGA-V1-A8MJ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-V1-A8ML       TCGA-V1-A8MM       TCGA-V1-A8MU       TCGA-V1-A8WL 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-V1-A8WV       TCGA-V1-A8X3       TCGA-VN-A88I       TCGA-VN-A88K 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VN-A88L       TCGA-VN-A88M       TCGA-VN-A88N       TCGA-VN-A88O 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VN-A88P       TCGA-VN-A88Q       TCGA-VN-A88R       TCGA-VP-A872 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A875       TCGA-VP-A876       TCGA-VP-A878       TCGA-VP-A879 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A87B       TCGA-VP-A87C       TCGA-VP-A87D       TCGA-VP-A87E 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A87H       TCGA-VP-A87J       TCGA-VP-A87K       TCGA-WW-A8ZI 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-X4-A8KQ       TCGA-XA-A8JR       TCGA-XJ-A83F       TCGA-XJ-A83G 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-XJ-A9DI       TCGA-XJ-A9DX       TCGA-Y6-A8TL       TCGA-YJ-A8SW 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8HK       TCGA-YL-A8HL       TCGA-YL-A8HM       TCGA-YL-A8HO 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8S8       TCGA-YL-A8S9       TCGA-YL-A8SA       TCGA-YL-A8SB 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8SC       TCGA-YL-A8SF       TCGA-YL-A8SH       TCGA-YL-A8SJ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8SK       TCGA-YL-A8SL       TCGA-YL-A8SQ       TCGA-YL-A8SR 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A9WH       TCGA-YL-A9WI       TCGA-YL-A9WJ       TCGA-YL-A9WK 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-ZG-A8QW       TCGA-ZG-A8QX       TCGA-ZG-A8QY       TCGA-ZG-A8QZ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
D29V8, continuous
D29V9, continuous
D29V10, continuous
D29V11, continuous
D29V12, continuous
D29V13, continuous
[1] "Remove cluster labels:" "GAGE2D MUTATED"        
clus
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               2              366 
      TCGA-2A-A8VL       TCGA-2A-A8VO       TCGA-2A-A8VT       TCGA-2A-A8VV 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-2A-A8VX       TCGA-2A-A8W1       TCGA-2A-A8W3       TCGA-CH-5737 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740       TCGA-CH-5741 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745       TCGA-CH-5746 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5750       TCGA-CH-5751       TCGA-CH-5752       TCGA-CH-5753 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5754       TCGA-CH-5761       TCGA-CH-5762       TCGA-CH-5763 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5764       TCGA-CH-5765       TCGA-CH-5766       TCGA-CH-5767 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5768       TCGA-CH-5769       TCGA-CH-5771       TCGA-CH-5772 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5788       TCGA-CH-5789       TCGA-CH-5790       TCGA-CH-5791 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5792       TCGA-CH-5794       TCGA-EJ-5495       TCGA-EJ-5496 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5502 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5503       TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5507       TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5511       TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5516       TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5521       TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5526       TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5532       TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7125       TCGA-EJ-7218       TCGA-EJ-7312       TCGA-EJ-7314 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7318       TCGA-EJ-7321 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7325       TCGA-EJ-7327       TCGA-EJ-7330       TCGA-EJ-7331 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7791 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-8468       TCGA-EJ-8469       TCGA-EJ-8472       TCGA-EJ-8474 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A46B       TCGA-EJ-A46D       TCGA-EJ-A46E       TCGA-EJ-A46F 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A46G       TCGA-EJ-A46H       TCGA-EJ-A46I       TCGA-EJ-A65B 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A65D       TCGA-EJ-A65E       TCGA-EJ-A65F       TCGA-EJ-A65G 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A65J       TCGA-EJ-A65M       TCGA-EJ-A6RA       TCGA-EJ-A6RC 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A7NF       TCGA-EJ-A7NG       TCGA-EJ-A7NH       TCGA-EJ-A7NJ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A7NK       TCGA-EJ-A7NM       TCGA-EJ-A7NN       TCGA-EJ-A8FN 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-A8FO       TCGA-EJ-A8FP       TCGA-EJ-A8FS       TCGA-FC-A5OB 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FC-A66V       TCGA-FC-A6HD       TCGA-FC-A8O0       TCGA-G9-6329 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6339       TCGA-G9-6342       TCGA-G9-6343       TCGA-G9-6347 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6354       TCGA-G9-6356 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6377       TCGA-G9-6378 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6379       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6498       TCGA-G9-6499       TCGA-G9-7510 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-7519       TCGA-G9-7521       TCGA-G9-7522       TCGA-G9-7523 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-7525       TCGA-H9-7775       TCGA-H9-A6BX       TCGA-HC-7075 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7212 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7736       TCGA-HC-7737 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7740       TCGA-HC-7744       TCGA-HC-7747       TCGA-HC-7748 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7817 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7818       TCGA-HC-7819       TCGA-HC-7821       TCGA-HC-8216 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-8257       TCGA-HC-8258       TCGA-HC-8259       TCGA-HC-8260 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-8262       TCGA-HC-8265       TCGA-HC-A76W       TCGA-HC-A76X 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-A8CY       TCGA-HC-A8D0       TCGA-HC-A8D1       TCGA-HI-7168 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HI-7169       TCGA-HI-7170       TCGA-HI-7171       TCGA-J4-8198 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-8200       TCGA-J4-A67K       TCGA-J4-A67L       TCGA-J4-A67M 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A67N       TCGA-J4-A67O       TCGA-J4-A67Q       TCGA-J4-A67R 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A67S       TCGA-J4-A67T       TCGA-J4-A6G1       TCGA-J4-A6G3 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A6M7       TCGA-J4-A83I       TCGA-J4-A83J       TCGA-J4-A83K 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J4-A83L       TCGA-J4-A83M       TCGA-J4-A83N       TCGA-J9-A52B 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J9-A52C       TCGA-J9-A52D       TCGA-J9-A52E       TCGA-J9-A8CL 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-J9-A8CM       TCGA-J9-A8CN       TCGA-J9-A8CP       TCGA-KC-A4BL 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A4BN       TCGA-KC-A4BO       TCGA-KC-A4BR       TCGA-KC-A4BV 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A7F3       TCGA-KC-A7F5       TCGA-KC-A7F6       TCGA-KC-A7FA 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KC-A7FD       TCGA-KC-A7FE       TCGA-KK-A59V       TCGA-KK-A59Y 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A59Z       TCGA-KK-A5A1       TCGA-KK-A6DY       TCGA-KK-A6E0 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A6E1       TCGA-KK-A6E2       TCGA-KK-A6E3       TCGA-KK-A6E4 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A6E5       TCGA-KK-A6E6       TCGA-KK-A6E7       TCGA-KK-A6E8 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7AQ       TCGA-KK-A7AU       TCGA-KK-A7AV       TCGA-KK-A7AW 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7AY       TCGA-KK-A7B0       TCGA-KK-A7B1       TCGA-KK-A7B2 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A7B3       TCGA-KK-A7B4       TCGA-KK-A8I4       TCGA-KK-A8I5 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8I6       TCGA-KK-A8I7       TCGA-KK-A8I8       TCGA-KK-A8I9 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8IA       TCGA-KK-A8IC       TCGA-KK-A8ID       TCGA-KK-A8IF 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8IG       TCGA-KK-A8IH       TCGA-KK-A8II       TCGA-KK-A8IJ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-KK-A8IK       TCGA-KK-A8IL       TCGA-KK-A8IM       TCGA-M7-A723 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QU-A6IL       TCGA-QU-A6IM       TCGA-QU-A6IN       TCGA-QU-A6IO 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-QU-A6IP       TCGA-SU-A7E7       TCGA-V1-A8MF       TCGA-V1-A8MG 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-V1-A8MJ       TCGA-V1-A8MK       TCGA-V1-A8ML       TCGA-V1-A8MM 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-V1-A8MU       TCGA-V1-A8WL       TCGA-V1-A8WN       TCGA-V1-A8WS 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-V1-A8WV       TCGA-V1-A8X3       TCGA-VN-A88I       TCGA-VN-A88K 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VN-A88L       TCGA-VN-A88N       TCGA-VN-A88O       TCGA-VN-A88P 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VN-A88Q       TCGA-VN-A88R       TCGA-VP-A872       TCGA-VP-A875 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A876       TCGA-VP-A878       TCGA-VP-A879       TCGA-VP-A87B 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A87C       TCGA-VP-A87D       TCGA-VP-A87E       TCGA-VP-A87H 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-VP-A87J       TCGA-VP-A87K       TCGA-WW-A8ZI       TCGA-X4-A8KQ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-X4-A8KS       TCGA-XA-A8JR       TCGA-XJ-A83F       TCGA-XJ-A83G 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-XJ-A83H       TCGA-XJ-A9DI       TCGA-XJ-A9DK       TCGA-XJ-A9DX 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-Y6-A8TL       TCGA-YJ-A8SW       TCGA-YL-A8HJ       TCGA-YL-A8HK 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8HL       TCGA-YL-A8HM       TCGA-YL-A8HO       TCGA-YL-A8S8 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8S9       TCGA-YL-A8SA       TCGA-YL-A8SB       TCGA-YL-A8SC 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8SF       TCGA-YL-A8SH       TCGA-YL-A8SJ       TCGA-YL-A8SK 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8SL       TCGA-YL-A8SO       TCGA-YL-A8SP       TCGA-YL-A8SQ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A8SR       TCGA-YL-A9WH       TCGA-YL-A9WI       TCGA-YL-A9WJ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-YL-A9WK       TCGA-ZG-A8QZ 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAGE2D MUTATED       0                         0     2
  GAGE2D WILD-TYPE     2                         7   145
D29V14, multiclass
[1] "Remove cluster labels:" "GAGE2D MUTATED"        
clus
  GAGE2D MUTATED GAGE2D WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5498 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503       TCGA-EJ-5504 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507       TCGA-EJ-5508 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511       TCGA-EJ-5512 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516       TCGA-EJ-5517 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521       TCGA-EJ-5522 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526       TCGA-EJ-5527 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532       TCGA-EJ-5542 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125       TCGA-EJ-7314 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321       TCGA-EJ-7327 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331       TCGA-EJ-7781 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784       TCGA-EJ-7785 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789       TCGA-EJ-7791 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794       TCGA-EJ-7797 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6351       TCGA-G9-6353       TCGA-G9-6356 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363       TCGA-G9-6364 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367       TCGA-G9-6369 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373       TCGA-G9-6377 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385       TCGA-G9-6494 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775       TCGA-HC-7075 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079       TCGA-HC-7080 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210       TCGA-HC-7211 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230       TCGA-HC-7231 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736       TCGA-HC-7737 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742       TCGA-HC-7744 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748       TCGA-HC-7749 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"GAGE2D WILD-TYPE" "GAGE2D WILD-TYPE" 

Clustering(30) Variable = EMG1 MUTATION ANALYSIS
D30V1, survival
                sevent
clus2              0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 408   7
  EMG1 MUTATED EMG1 WILD-TYPE 
             4            415 
  EMG1 MUTATED EMG1 WILD-TYPE 
             0              7 
$`EMG1 MUTATED`
TCGA-HC-7078 TCGA-HC-7752 TCGA-VP-A872 TCGA-VP-A876 
       65.26        25.71       111.39       109.58 

$`EMG1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 
       32.68         6.08        30.94         3.68        19.76         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7817 TCGA-HC-7818 
       24.59        26.04         1.97        17.16        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A875 
       15.52        15.81        41.42        44.91        25.78        75.91 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  EMG1 MUTATED EMG1 WILD-TYPE 
         25.71           0.72 
  EMG1 MUTATED EMG1 WILD-TYPE 
        111.39         165.17 
  EMG1 MUTATED EMG1 WILD-TYPE 
         87.42          27.19 
[1] "25.7 - 111.4 (87.4)" "0.7 - 165.2 (27.2)" 
[1] "hr="     "9400000"
D30V2, continuous
                vv
clus              T2  T3  T4
  EMG1 MUTATED     2   2   0
  EMG1 WILD-TYPE 170 237   6
D30V3, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  T2            2            170
  T3            2            237
  T4            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"
D30V4, binary
                cls
clus               0   1
  EMG1 MUTATED     4   0
  EMG1 WILD-TYPE 295  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      4    0
  EMG1 WILD-TYPE  295   58
   clus
vv  EMG1 MUTATED EMG1 WILD-TYPE
  0            4            295
  1            0             58
[1] 2 2
[1] FALSE
D30V5, binary
                cls
clus               0   1
  EMG1 MUTATED     1   3
  EMG1 WILD-TYPE  14 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  EMG1 MUTATED      1    3
  EMG1 WILD-TYPE   14  402
                                        clus
vv                                       EMG1 MUTATED EMG1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EMG1 MUTATED     4   0   0   0
  EMG1 WILD-TYPE 279 103   5  15
D30V6, multiclass
    clus
vv   EMG1 MUTATED EMG1 WILD-TYPE
  R0            4            279
  R1            0            103
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, continuous
D30V8, continuous
D30V9, continuous
D30V10, continuous
D30V11, continuous
D30V12, continuous
D30V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EMG1 MUTATED       0                         0     2
  EMG1 WILD-TYPE     2                         7   145
D30V14, multiclass
[1] "Remove cluster labels:" "EMG1 MUTATED"          
clus
  EMG1 MUTATED EMG1 WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6353     TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6373     TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-G9-6385     TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-H9-7775     TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7079 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7231     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7818     TCGA-HC-7819 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"EMG1 WILD-TYPE" "EMG1 WILD-TYPE" 

Clustering(31) Variable = LAMA3 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2               0   1
  LAMA3 MUTATED     7   0
  LAMA3 WILD-TYPE 405   7
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              7             412 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              0               7 
$`LAMA3 MUTATED`
TCGA-EJ-7797 TCGA-HC-8264 TCGA-HC-A6AQ TCGA-J4-A83J TCGA-KK-A6E8 TCGA-VN-A88M 
       19.92         1.58         3.48        22.88        58.19         6.21 
TCGA-YL-A9WK 
       62.37 

$`LAMA3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 
       19.59        17.29         3.75        23.05        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
       22.32        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AS 
        2.01         2.20         1.61        17.42         2.33         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       16.83        22.52        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
       49.25       113.33        67.07         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       25.51        24.53        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  LAMA3 MUTATED LAMA3 WILD-TYPE 
           1.58            0.72 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
          62.37          165.17 
  LAMA3 MUTATED LAMA3 WILD-TYPE 
         19.920          27.485 
[1] "1.6 - 62.4 (19.9)"  "0.7 - 165.2 (27.5)"
[1] "hr="     "9100000"
D31V2, continuous
                 vv
clus               T2  T3  T4
  LAMA3 MUTATED     5   2   0
  LAMA3 WILD-TYPE 167 237   6
D31V3, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  T2             5             167
  T3             2             237
  T4             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"
D31V4, binary
                 cls
clus                0   1
  LAMA3 MUTATED     5   1
  LAMA3 WILD-TYPE 294  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      5    1
  LAMA3 WILD-TYPE  294   57
   clus
vv  LAMA3 MUTATED LAMA3 WILD-TYPE
  0             5             294
  1             1              57
[1] 2 2
[1] FALSE
D31V5, binary
                 cls
clus                0   1
  LAMA3 MUTATED     0   7
  LAMA3 WILD-TYPE  15 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LAMA3 MUTATED      0    7
  LAMA3 WILD-TYPE   15  398
                                        clus
vv                                       LAMA3 MUTATED LAMA3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             398
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LAMA3 MUTATED     3   3   0   1
  LAMA3 WILD-TYPE 280 100   5  14
D31V6, multiclass
    clus
vv   LAMA3 MUTATED LAMA3 WILD-TYPE
  R0             3             280
  R1             3             100
  R2             0               5
  RX             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, continuous
D31V8, continuous
D31V9, continuous
D31V10, continuous
D31V11, continuous
D31V12, continuous
D31V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LAMA3 MUTATED       0                         0     1
  LAMA3 WILD-TYPE     2                         7   146
D31V14, multiclass
[1] "Remove cluster labels:" "LAMA3 MUTATED"         
clus
  LAMA3 MUTATED LAMA3 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" "LAMA3 WILD-TYPE" 

Clustering(32) Variable = RPL11 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2               0   1
  RPL11 MUTATED     4   0
  RPL11 WILD-TYPE 408   7
  RPL11 MUTATED RPL11 WILD-TYPE 
              4             415 
  RPL11 MUTATED RPL11 WILD-TYPE 
              0               7 
$`RPL11 MUTATED`
TCGA-EJ-A65B TCGA-HC-7081 TCGA-M7-A722 TCGA-V1-A8WS 
       23.34        37.35        34.85        15.58 

$`RPL11 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.23        25.74        21.96        23.80        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       36.36        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A723 TCGA-M7-A724 
        5.19        21.14        12.62        13.15        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WV TCGA-V1-A8X3 
       39.29        53.16        52.08        30.38        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  RPL11 MUTATED RPL11 WILD-TYPE 
          15.58            0.72 
  RPL11 MUTATED RPL11 WILD-TYPE 
          37.35          165.17 
  RPL11 MUTATED RPL11 WILD-TYPE 
         29.095          27.290 
[1] "15.6 - 37.4 (29.1)" "0.7 - 165.2 (27.3)"
[1] "hr="     "3300000"
D32V2, continuous
                 vv
clus               T2  T3  T4
  RPL11 MUTATED     0   4   0
  RPL11 WILD-TYPE 172 235   6
D32V3, multiclass
    clus
vv   RPL11 MUTATED RPL11 WILD-TYPE
  T2             0             172
  T3             4             235
  T4             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"
D32V4, binary
                 cls
clus                0   1
  RPL11 MUTATED     2   0
  RPL11 WILD-TYPE 297  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL11 MUTATED      2    0
  RPL11 WILD-TYPE  297   58
   clus
vv  RPL11 MUTATED RPL11 WILD-TYPE
  0             2             297
  1             0              58
[1] 2 2
[1] FALSE
D32V5, binary
                 cls
clus                0   1
  RPL11 MUTATED     1   3
  RPL11 WILD-TYPE  14 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RPL11 MUTATED      1    3
  RPL11 WILD-TYPE   14  402
                                        clus
vv                                       RPL11 MUTATED RPL11 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1              14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             402
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RPL11 MUTATED     1   2   1   0
  RPL11 WILD-TYPE 282 101   4  15
D32V6, multiclass
    clus
vv   RPL11 MUTATED RPL11 WILD-TYPE
  R0             1             282
  R1             2             101
  R2             1               4
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, continuous
[1] "Remove cluster labels:" "RPL11 MUTATED"         
clus
  RPL11 MUTATED RPL11 WILD-TYPE 
              2             340 
     TCGA-2A-A8VL      TCGA-2A-A8VT      TCGA-2A-A8VV      TCGA-2A-A8VX 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-2A-A8W1      TCGA-2A-A8W3      TCGA-CH-5737      TCGA-CH-5739 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5740      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7218      TCGA-EJ-7312 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7325      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7794 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8470 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-8472      TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A65D 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G      TCGA-EJ-A65J 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-EJ-A6RA      TCGA-EJ-A6RC      TCGA-EJ-A7NF 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A7NG      TCGA-EJ-A7NJ      TCGA-EJ-A7NK      TCGA-EJ-A7NM 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A7NN      TCGA-EJ-A8FN      TCGA-EJ-A8FO      TCGA-EJ-A8FP 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A8FS      TCGA-EJ-A8FU      TCGA-FC-7708      TCGA-FC-7961 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-FC-A5OB      TCGA-FC-A66V      TCGA-FC-A6HD      TCGA-FC-A8O0 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6339      TCGA-G9-6348      TCGA-G9-6356      TCGA-G9-6361 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6377 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6494      TCGA-G9-6496 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6499      TCGA-G9-7510      TCGA-G9-7521      TCGA-G9-7522 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-7523      TCGA-G9-7525      TCGA-H9-A6BY      TCGA-HC-7078 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7209      TCGA-HC-7210 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737      TCGA-HC-7740 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7742      TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7752      TCGA-HC-7818 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7821      TCGA-HC-8216      TCGA-HC-8257 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-8258      TCGA-HC-8260      TCGA-HC-8262      TCGA-HC-8264 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-8265      TCGA-HC-8266      TCGA-HC-A48F      TCGA-HC-A4ZV 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-A631      TCGA-HC-A632      TCGA-HC-A6AL      TCGA-HC-A6AN 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-A6AS      TCGA-HC-A6HX      TCGA-HC-A76W      TCGA-HC-A76X 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-A8CY      TCGA-HC-A8D0      TCGA-HC-A8D1      TCGA-HI-7168 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171      TCGA-J4-8200 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A67L      TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A67R      TCGA-J4-A67S      TCGA-J4-A6G1      TCGA-J4-A6G3 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A83I      TCGA-J4-A83J      TCGA-J4-A83L      TCGA-J4-A83M 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J9-A52B      TCGA-J9-A52E      TCGA-J9-A8CM      TCGA-KC-A4BL 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR      TCGA-KC-A4BV 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A7F3      TCGA-KC-A7F5      TCGA-KC-A7F6      TCGA-KC-A7FA 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A7FD      TCGA-KC-A7FE      TCGA-KK-A59V      TCGA-KK-A59X 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A59Y      TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E0      TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E4      TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E8      TCGA-KK-A7AP      TCGA-KK-A7AQ      TCGA-KK-A7AU 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A7AV      TCGA-KK-A7AW      TCGA-KK-A7AY      TCGA-KK-A7AZ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A7B0      TCGA-KK-A7B1      TCGA-KK-A7B2      TCGA-KK-A7B3 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A7B4      TCGA-KK-A8I4      TCGA-KK-A8I6      TCGA-KK-A8I7 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A8IA      TCGA-KK-A8ID      TCGA-KK-A8IJ      TCGA-KK-A8IL 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-M7-A71Z      TCGA-M7-A723      TCGA-M7-A724      TCGA-M7-A725 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN      TCGA-QU-A6IO 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-QU-A6IP      TCGA-SU-A7E7      TCGA-V1-A8MF      TCGA-V1-A8MJ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-V1-A8ML      TCGA-V1-A8MM      TCGA-V1-A8MU      TCGA-V1-A8WL 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-V1-A8WV      TCGA-V1-A8X3      TCGA-VN-A88I      TCGA-VN-A88K 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VN-A88L      TCGA-VN-A88M      TCGA-VN-A88N      TCGA-VN-A88O 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VN-A88P      TCGA-VN-A88Q      TCGA-VN-A88R      TCGA-VP-A872 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A875      TCGA-VP-A876      TCGA-VP-A878      TCGA-VP-A879 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A87B      TCGA-VP-A87C      TCGA-VP-A87D      TCGA-VP-A87E 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A87H      TCGA-VP-A87J      TCGA-VP-A87K      TCGA-WW-A8ZI 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-X4-A8KQ      TCGA-XA-A8JR      TCGA-XJ-A83F      TCGA-XJ-A83G 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-XJ-A9DI      TCGA-XJ-A9DX      TCGA-Y6-A8TL      TCGA-YJ-A8SW 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8HK      TCGA-YL-A8HL      TCGA-YL-A8HM      TCGA-YL-A8HO 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8S8      TCGA-YL-A8S9      TCGA-YL-A8SA      TCGA-YL-A8SB 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8SC      TCGA-YL-A8SF      TCGA-YL-A8SH      TCGA-YL-A8SJ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8SK      TCGA-YL-A8SL      TCGA-YL-A8SQ      TCGA-YL-A8SR 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A9WH      TCGA-YL-A9WI      TCGA-YL-A9WJ      TCGA-YL-A9WK 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-ZG-A8QW      TCGA-ZG-A8QX      TCGA-ZG-A8QY      TCGA-ZG-A8QZ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
D32V8, continuous
D32V9, continuous
D32V10, continuous
D32V11, continuous
D32V12, continuous
D32V13, continuous
[1] "Remove cluster labels:" "RPL11 MUTATED"         
clus
  RPL11 MUTATED RPL11 WILD-TYPE 
              2             366 
     TCGA-2A-A8VL      TCGA-2A-A8VO      TCGA-2A-A8VT      TCGA-2A-A8VV 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-2A-A8VX      TCGA-2A-A8W1      TCGA-2A-A8W3      TCGA-CH-5737 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740      TCGA-CH-5741 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745      TCGA-CH-5746 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5768      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5495      TCGA-EJ-5496 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7218      TCGA-EJ-7312 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7318 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7321      TCGA-EJ-7325      TCGA-EJ-7327      TCGA-EJ-7330 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469      TCGA-EJ-8472 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-8474      TCGA-EJ-A46B      TCGA-EJ-A46D      TCGA-EJ-A46E 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A46F      TCGA-EJ-A46G      TCGA-EJ-A46H      TCGA-EJ-A46I 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A65D      TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A65J      TCGA-EJ-A65M      TCGA-EJ-A6RA      TCGA-EJ-A6RC 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A7NF      TCGA-EJ-A7NG      TCGA-EJ-A7NH      TCGA-EJ-A7NJ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A7NK      TCGA-EJ-A7NM      TCGA-EJ-A7NN      TCGA-EJ-A8FN 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-A8FO      TCGA-EJ-A8FP      TCGA-EJ-A8FS      TCGA-FC-A5OB 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-FC-A66V      TCGA-FC-A6HD      TCGA-FC-A8O0      TCGA-G9-6329 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6339      TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6347 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6354 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6377 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6385 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6498      TCGA-G9-6499 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-7510      TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-7523      TCGA-G9-7525      TCGA-H9-7775      TCGA-H9-A6BX 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7736 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7740      TCGA-HC-7744      TCGA-HC-7747 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7748      TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7817      TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7821 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-8216      TCGA-HC-8257      TCGA-HC-8258      TCGA-HC-8259 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-8260      TCGA-HC-8262      TCGA-HC-8265      TCGA-HC-A76W 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-A76X      TCGA-HC-A8CY      TCGA-HC-A8D0      TCGA-HC-A8D1 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-8198      TCGA-J4-8200      TCGA-J4-A67K      TCGA-J4-A67L 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O      TCGA-J4-A67Q 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A67R      TCGA-J4-A67S      TCGA-J4-A67T      TCGA-J4-A6G1 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A6G3      TCGA-J4-A6M7      TCGA-J4-A83I      TCGA-J4-A83J 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J4-A83K      TCGA-J4-A83L      TCGA-J4-A83M      TCGA-J4-A83N 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J9-A52B      TCGA-J9-A52C      TCGA-J9-A52D      TCGA-J9-A52E 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-J9-A8CL      TCGA-J9-A8CM      TCGA-J9-A8CN      TCGA-J9-A8CP 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO      TCGA-KC-A4BR 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A4BV      TCGA-KC-A7F3      TCGA-KC-A7F5      TCGA-KC-A7F6 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KC-A7FA      TCGA-KC-A7FD      TCGA-KC-A7FE      TCGA-KK-A59V 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A59Y      TCGA-KK-A59Z      TCGA-KK-A5A1      TCGA-KK-A6DY 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E0      TCGA-KK-A6E1      TCGA-KK-A6E2      TCGA-KK-A6E3 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E4      TCGA-KK-A6E5      TCGA-KK-A6E6      TCGA-KK-A6E7 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A6E8      TCGA-KK-A7AQ      TCGA-KK-A7AU      TCGA-KK-A7AV 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A7AW      TCGA-KK-A7AY      TCGA-KK-A7B0      TCGA-KK-A7B1 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A7B2      TCGA-KK-A7B3      TCGA-KK-A7B4      TCGA-KK-A8I4 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A8I5      TCGA-KK-A8I6      TCGA-KK-A8I7      TCGA-KK-A8I8 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A8I9      TCGA-KK-A8IA      TCGA-KK-A8IC      TCGA-KK-A8ID 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A8IF      TCGA-KK-A8IG      TCGA-KK-A8IH      TCGA-KK-A8II 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-KK-A8IJ      TCGA-KK-A8IK      TCGA-KK-A8IL      TCGA-KK-A8IM 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-M7-A723      TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-QU-A6IO      TCGA-QU-A6IP      TCGA-SU-A7E7      TCGA-V1-A8MF 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-V1-A8MG      TCGA-V1-A8MJ      TCGA-V1-A8MK      TCGA-V1-A8ML 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-V1-A8MM      TCGA-V1-A8MU      TCGA-V1-A8WL      TCGA-V1-A8WN 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-V1-A8WV      TCGA-V1-A8X3      TCGA-VN-A88I      TCGA-VN-A88K 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VN-A88L      TCGA-VN-A88N      TCGA-VN-A88O      TCGA-VN-A88P 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VN-A88Q      TCGA-VN-A88R      TCGA-VP-A872      TCGA-VP-A875 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A876      TCGA-VP-A878      TCGA-VP-A879      TCGA-VP-A87B 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A87C      TCGA-VP-A87D      TCGA-VP-A87E      TCGA-VP-A87H 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-VP-A87J      TCGA-VP-A87K      TCGA-WW-A8ZI      TCGA-X4-A8KQ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-X4-A8KS      TCGA-XA-A8JR      TCGA-XJ-A83F      TCGA-XJ-A83G 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-XJ-A83H      TCGA-XJ-A9DI      TCGA-XJ-A9DK      TCGA-XJ-A9DX 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-Y6-A8TL      TCGA-YJ-A8SW      TCGA-YL-A8HJ      TCGA-YL-A8HK 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8HL      TCGA-YL-A8HM      TCGA-YL-A8HO      TCGA-YL-A8S8 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8S9      TCGA-YL-A8SA      TCGA-YL-A8SB      TCGA-YL-A8SC 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8SF      TCGA-YL-A8SH      TCGA-YL-A8SJ      TCGA-YL-A8SK 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8SL      TCGA-YL-A8SO      TCGA-YL-A8SP      TCGA-YL-A8SQ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A8SR      TCGA-YL-A9WH      TCGA-YL-A9WI      TCGA-YL-A9WJ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-YL-A9WK      TCGA-ZG-A8QZ 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RPL11 MUTATED       0                         0     1
  RPL11 WILD-TYPE     2                         7   146
D32V14, multiclass
[1] "Remove cluster labels:" "RPL11 MUTATED"         
clus
  RPL11 MUTATED RPL11 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-EJ-7797      TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6332      TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6353      TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6363      TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-G9-6385      TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-H9-7775      TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7079      TCGA-HC-7080      TCGA-HC-7209      TCGA-HC-7210 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"RPL11 WILD-TYPE" "RPL11 WILD-TYPE" "RPL11 WILD-TYPE" 

Clustering(33) Variable = ZFHX3 MUTATION ANALYSIS
D33V1, survival
                 sevent
clus2               0   1
  ZFHX3 MUTATED    13   0
  ZFHX3 WILD-TYPE 399   7
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
             13             406 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
              0               7 
$`ZFHX3 MUTATED`
TCGA-2A-A8VX TCGA-EJ-5507 TCGA-EJ-7782 TCGA-EJ-A65J TCGA-EJ-A7NM TCGA-G9-6499 
       33.96        23.90        38.37        14.83         4.21        50.73 
TCGA-HC-7738 TCGA-HC-7820 TCGA-J9-A52C TCGA-KC-A7FD TCGA-VN-A88R TCGA-VP-A87E 
       31.69        24.56         5.85         8.88        25.78        66.97 
TCGA-YL-A9WH 
       14.04 

$`ZFHX3 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8W1 TCGA-2A-A8W3 
       20.42        43.79        32.71        22.06         3.68        25.35 
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       30.31        27.19        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        6.28        24.39        23.90        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG 
       21.90         7.56        11.61        28.70         8.22        14.20 
TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
       15.58         6.48        15.65         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.83         8.75         4.54        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       64.18        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       32.68         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        0.72         2.10        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       30.84        17.85        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       14.37        20.28        13.87         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       41.42        44.91       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87H TCGA-VP-A87J 
       23.93        85.18        55.56        60.92        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK 
       71.34        62.79         8.98        53.36        60.99        62.37 
TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
        3.09        14.53        13.28        10.13 

  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
           4.21            0.72 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
          66.97          165.17 
  ZFHX3 MUTATED ZFHX3 WILD-TYPE 
         24.560          27.485 
[1] "4.2 - 67.0 (24.6)"  "0.7 - 165.2 (27.5)"
[1] "hr="     "9300000"
D33V2, continuous
                 vv
clus               T2  T3  T4
  ZFHX3 MUTATED     5   8   0
  ZFHX3 WILD-TYPE 167 231   6
D33V3, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  T2             5             167
  T3             8             231
  T4             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"
D33V4, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     7   3
  ZFHX3 WILD-TYPE 292  55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      7    3
  ZFHX3 WILD-TYPE  292   55
   clus
vv  ZFHX3 MUTATED ZFHX3 WILD-TYPE
  0             7             292
  1             3              55
[1] 2 2
[1] FALSE
D33V5, binary
                 cls
clus                0   1
  ZFHX3 MUTATED     1  12
  ZFHX3 WILD-TYPE  14 393
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX3 MUTATED      1   12
  ZFHX3 WILD-TYPE   14  393
                                        clus
vv                                       ZFHX3 MUTATED ZFHX3 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1              14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               12             393
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ZFHX3 MUTATED    12   1   0   0
  ZFHX3 WILD-TYPE 271 102   5  15
D33V6, multiclass
    clus
vv   ZFHX3 MUTATED ZFHX3 WILD-TYPE
  R0            12             271
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, continuous
D33V8, continuous
D33V9, continuous
D33V10, continuous
D33V11, continuous
D33V12, continuous
D33V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZFHX3 MUTATED       0                         1     4
  ZFHX3 WILD-TYPE     2                         6   143
D33V14, multiclass
                           clus
vv                          ZFHX3 MUTATED ZFHX3 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 4             143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = MUC17 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2               0   1
  MUC17 MUTATED    22   1
  MUC17 WILD-TYPE 390   6
  MUC17 MUTATED MUC17 WILD-TYPE 
             23             396 
  MUC17 MUTATED MUC17 WILD-TYPE 
              1               6 
$`MUC17 MUTATED`
TCGA-CH-5748 TCGA-EJ-5514 TCGA-EJ-7218 TCGA-EJ-7321 TCGA-EJ-7782 TCGA-EJ-8469 
        1.02        36.23        83.57        27.09        38.37        76.41 
TCGA-EJ-A65B TCGA-EJ-A65J TCGA-FC-7961 TCGA-HC-A8D0 TCGA-J4-A67K TCGA-KK-A6E3 
       23.34        14.83        15.42        25.48        33.01        67.59 
TCGA-KK-A6E8 TCGA-KK-A7AU TCGA-KK-A7AZ TCGA-M7-A721 TCGA-QU-A6IM TCGA-VP-A878 
       58.19        58.36        49.94        13.15        41.00        97.41 
TCGA-VP-A879 TCGA-VP-A87D TCGA-YL-A8SC TCGA-YL-A8SP TCGA-ZG-A8QY 
       23.93        60.92        41.46        71.34        13.28 

$`MUC17 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97         2.99        24.03        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       48.53        38.53        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       74.10        93.70        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
       33.83        35.18        30.35        27.68         6.28        24.39 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       23.90        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       77.16        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D 
       17.23        25.74        21.96        23.80        21.96        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        18.41        21.90         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       28.41        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D1 
        1.25         4.41         7.00         4.93         9.53        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       30.02        54.54       165.17       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
       67.07         6.44        52.93        27.02        34.65        51.68 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       21.14        12.62        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
        3.19       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A87B 
       44.91        25.78       111.39        75.91       109.58        85.18 
TCGA-VP-A87C TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       55.56        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         2.99        31.99        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       60.56        16.83        56.52        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29        32.45       114.38        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QZ 
       53.36        60.99        62.37         3.09        14.53        10.13 

  MUC17 MUTATED MUC17 WILD-TYPE 
           1.02            0.72 
  MUC17 MUTATED MUC17 WILD-TYPE 
          97.41          165.17 
  MUC17 MUTATED MUC17 WILD-TYPE 
          38.37           27.09 
[1] "1.0 - 97.4 (38.4)"  "0.7 - 165.2 (27.1)"
[1] "hr=" "3"  
D34V2, continuous
                 vv
clus               T2  T3  T4
  MUC17 MUTATED    11  12   0
  MUC17 WILD-TYPE 161 227   6
D34V3, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  T2            11             161
  T3            12             227
  T4             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"
D34V4, binary
                 cls
clus                0   1
  MUC17 MUTATED    16   4
  MUC17 WILD-TYPE 283  54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED     16    4
  MUC17 WILD-TYPE  283   54
   clus
vv  MUC17 MUTATED MUC17 WILD-TYPE
  0            16             283
  1             4              54
[1] 2 2
[1] FALSE
D34V5, binary
                 cls
clus                0   1
  MUC17 MUTATED     1  22
  MUC17 WILD-TYPE  14 383
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MUC17 MUTATED      1   22
  MUC17 WILD-TYPE   14  383
                                        clus
vv                                       MUC17 MUTATED MUC17 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1              14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               22             383
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MUC17 MUTATED    12   7   0   3
  MUC17 WILD-TYPE 271  96   5  12
D34V6, multiclass
    clus
vv   MUC17 MUTATED MUC17 WILD-TYPE
  R0            12             271
  R1             7              96
  R2             0               5
  RX             3              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, continuous
D34V8, continuous
D34V9, continuous
D34V10, continuous
D34V11, continuous
D34V12, continuous
D34V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MUC17 MUTATED       0                         2     3
  MUC17 WILD-TYPE     2                         5   144
D34V14, multiclass
                           clus
vv                          MUC17 MUTATED MUC17 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             2               5
  WHITE                                 3             144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = CDKN1B MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2                0   1
  CDKN1B MUTATED     5   0
  CDKN1B WILD-TYPE 407   7
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               5              414 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
               0                7 
$`CDKN1B MUTATED`
TCGA-CH-5752 TCGA-EJ-5518 TCGA-EJ-7786 TCGA-KK-A59V TCGA-VP-A87J 
       31.00        52.27        14.53       113.10        53.36 

$`CDKN1B WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       35.01         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       20.55        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 
       10.82         9.27         9.83         8.75         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  CDKN1B MUTATED CDKN1B WILD-TYPE 
           14.53             0.72 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
          113.10           165.17 
  CDKN1B MUTATED CDKN1B WILD-TYPE 
          52.270           27.175 
[1] "14.5 - 113.1 (52.3)" "0.7 - 165.2 (27.2)" 
[1] "hr="     "9200000"
D35V2, continuous
                  vv
clus                T2  T3  T4
  CDKN1B MUTATED     1   3   1
  CDKN1B WILD-TYPE 171 236   5
D35V3, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  T2              1              171
  T3              3              236
  T4              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"
D35V4, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     4   1
  CDKN1B WILD-TYPE 295  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      4    1
  CDKN1B WILD-TYPE  295   57
   clus
vv  CDKN1B MUTATED CDKN1B WILD-TYPE
  0              4              295
  1              1               57
[1] 2 2
[1] FALSE
D35V5, binary
                  cls
clus                 0   1
  CDKN1B MUTATED     0   5
  CDKN1B WILD-TYPE  15 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1B MUTATED      0    5
  CDKN1B WILD-TYPE   15  400
                                        clus
vv                                       CDKN1B MUTATED CDKN1B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              400
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  CDKN1B MUTATED     3   1   1   0
  CDKN1B WILD-TYPE 280 102   4  15
D35V6, multiclass
    clus
vv   CDKN1B MUTATED CDKN1B WILD-TYPE
  R0              3              280
  R1              1              102
  R2              1                4
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, continuous
D35V8, continuous
D35V9, continuous
D35V10, continuous
D35V11, continuous
D35V12, continuous
D35V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN1B MUTATED       0                         0     3
  CDKN1B WILD-TYPE     2                         7   144
D35V14, multiclass
                           clus
vv                          CDKN1B MUTATED CDKN1B WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = POM121 MUTATION ANALYSIS
D36V1, survival
                  sevent
clus2                0   1
  POM121 MUTATED     3   0
  POM121 WILD-TYPE 409   7
  POM121 MUTATED POM121 WILD-TYPE 
               3              416 
  POM121 MUTATED POM121 WILD-TYPE 
               0                7 
$`POM121 MUTATED`
TCGA-EJ-7797 TCGA-EJ-A65B TCGA-VN-A88O 
       19.92        23.34        15.81 

$`POM121 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-8468 TCGA-EJ-8469 
       19.59        17.29         3.75        23.05        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        21.96        23.80        21.96        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.52        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  POM121 MUTATED POM121 WILD-TYPE 
           15.81             0.72 
  POM121 MUTATED POM121 WILD-TYPE 
           23.34           165.17 
  POM121 MUTATED POM121 WILD-TYPE 
          19.920           27.485 
[1] "15.8 - 23.3 (19.9)" "0.7 - 165.2 (27.5)"
[1] "hr="    "440000"
D36V2, continuous
                  vv
clus                T2  T3  T4
  POM121 MUTATED     2   1   0
  POM121 WILD-TYPE 170 238   6
D36V3, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  T2              2              170
  T3              1              238
  T4              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"
D36V4, binary
                  cls
clus                 0   1
  POM121 MUTATED     3   0
  POM121 WILD-TYPE 296  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      3    0
  POM121 WILD-TYPE  296   58
   clus
vv  POM121 MUTATED POM121 WILD-TYPE
  0              3              296
  1              0               58
[1] 2 2
[1] FALSE
D36V5, binary
                  cls
clus                 0   1
  POM121 MUTATED     1   2
  POM121 WILD-TYPE  14 403
[1] "tbl2"
                  cls
clus               [,1] [,2]
  POM121 MUTATED      1    2
  POM121 WILD-TYPE   14  403
                                        clus
vv                                       POM121 MUTATED POM121 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1               14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 2              403
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  POM121 MUTATED     2   1   0   0
  POM121 WILD-TYPE 281 102   5  15
D36V6, multiclass
    clus
vv   POM121 MUTATED POM121 WILD-TYPE
  R0              2              281
  R1              1              102
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, continuous
D36V8, continuous
D36V9, continuous
D36V10, continuous
D36V11, continuous
D36V12, continuous
D36V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  POM121 MUTATED       0                         0     1
  POM121 WILD-TYPE     2                         7   146
D36V14, multiclass
[1] "Remove cluster labels:" "POM121 MUTATED"        
clus
  POM121 MUTATED POM121 WILD-TYPE 
               1              155 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329       TCGA-G9-6332 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338       TCGA-G9-6342 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 
      TCGA-HI-7169       TCGA-HI-7170       TCGA-HI-7171 
"POM121 WILD-TYPE" "POM121 WILD-TYPE" "POM121 WILD-TYPE" 

Clustering(37) Variable = ESCO1 MUTATION ANALYSIS
D37V1, survival
                 sevent
clus2               0   1
  ESCO1 MUTATED     4   0
  ESCO1 WILD-TYPE 408   7
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              4             415 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
              0               7 
$`ESCO1 MUTATED`
TCGA-CH-5765 TCGA-CH-5792 TCGA-EJ-5508 TCGA-HC-7747 
       23.01         2.99        38.93        24.59 

$`ESCO1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
       12.00         1.02         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       27.19        23.90        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       36.23        60.23        46.55        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 
       10.82         9.27         9.83         8.75         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.48         1.68        23.70        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 
        2.27        22.55        17.95        22.32         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  ESCO1 MUTATED ESCO1 WILD-TYPE 
           2.99            0.72 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          38.93          165.17 
  ESCO1 MUTATED ESCO1 WILD-TYPE 
          23.80           27.39 
[1] "3.0 - 38.9 (23.8)"  "0.7 - 165.2 (27.4)"
[1] "hr="     "3300000"
D37V2, continuous
                 vv
clus               T2  T3  T4
  ESCO1 MUTATED     1   3   0
  ESCO1 WILD-TYPE 171 236   6
D37V3, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  T2             1             171
  T3             3             236
  T4             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"
D37V4, binary
                 cls
clus                0   1
  ESCO1 MUTATED     4   0
  ESCO1 WILD-TYPE 295  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      4    0
  ESCO1 WILD-TYPE  295   58
   clus
vv  ESCO1 MUTATED ESCO1 WILD-TYPE
  0             4             295
  1             0              58
[1] 2 2
[1] FALSE
D37V5, binary
                 cls
clus                0   1
  ESCO1 MUTATED     0   4
  ESCO1 WILD-TYPE  15 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESCO1 MUTATED      0    4
  ESCO1 WILD-TYPE   15  401
                                        clus
vv                                       ESCO1 MUTATED ESCO1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             401
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  ESCO1 MUTATED     2   1   0   0
  ESCO1 WILD-TYPE 281 102   5  15
D37V6, multiclass
    clus
vv   ESCO1 MUTATED ESCO1 WILD-TYPE
  R0             2             281
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, continuous
D37V8, continuous
D37V9, continuous
D37V10, continuous
D37V11, continuous
D37V12, continuous
D37V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ESCO1 MUTATED       0                         0     4
  ESCO1 WILD-TYPE     2                         7   143
D37V14, multiclass
                           clus
vv                          ESCO1 MUTATED ESCO1 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 4             143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = MYOT MUTATION ANALYSIS
D38V1, survival
                sevent
clus2              0   1
  MYOT MUTATED     4   0
  MYOT WILD-TYPE 408   7
  MYOT MUTATED MYOT WILD-TYPE 
             4            415 
  MYOT MUTATED MYOT WILD-TYPE 
             0              7 
$`MYOT MUTATED`
TCGA-J9-A52D TCGA-KK-A59V TCGA-V1-A8WL TCGA-ZG-A8QY 
        6.97       113.10        52.08        13.28 

$`MYOT WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       32.68         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
       10.78        23.67        14.37        20.28        13.87         5.85 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y 
        8.65        19.66         8.88        11.57        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       14.73        39.29        53.16        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QZ 
       10.13 

  MYOT MUTATED MYOT WILD-TYPE 
          6.97           0.72 
  MYOT MUTATED MYOT WILD-TYPE 
        113.10         165.17 
  MYOT MUTATED MYOT WILD-TYPE 
         32.68          27.29 
[1] "7.0 - 113.1 (32.7)" "0.7 - 165.2 (27.3)"
[1] "hr="     "9100000"
D38V2, continuous
                vv
clus              T2  T3  T4
  MYOT MUTATED     0   4   0
  MYOT WILD-TYPE 172 235   6
D38V3, multiclass
    clus
vv   MYOT MUTATED MYOT WILD-TYPE
  T2            0            172
  T3            4            235
  T4            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"
D38V4, binary
                cls
clus               0   1
  MYOT MUTATED     2   1
  MYOT WILD-TYPE 297  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOT MUTATED      2    1
  MYOT WILD-TYPE  297   57
   clus
vv  MYOT MUTATED MYOT WILD-TYPE
  0            2            297
  1            1             57
[1] 2 2
[1] FALSE
D38V5, binary
                cls
clus               0   1
  MYOT MUTATED     1   3
  MYOT WILD-TYPE  14 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  MYOT MUTATED      1    3
  MYOT WILD-TYPE   14  402
                                        clus
vv                                       MYOT MUTATED MYOT WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            1             14
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  MYOT MUTATED     3   0   0   1
  MYOT WILD-TYPE 280 103   5  14
D38V6, multiclass
    clus
vv   MYOT MUTATED MYOT WILD-TYPE
  R0            3            280
  R1            0            103
  R2            0              5
  RX            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, continuous
D38V8, continuous
D38V9, continuous
D38V10, continuous
D38V11, continuous
D38V12, continuous
D38V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MYOT MUTATED       0                         0     0
  MYOT WILD-TYPE     2                         7   147
D38V14, multiclass

Clustering(39) Variable = L1CAM MUTATION ANALYSIS
D39V1, survival
                 sevent
clus2               0   1
  L1CAM MUTATED     5   1
  L1CAM WILD-TYPE 407   6
  L1CAM MUTATED L1CAM WILD-TYPE 
              6             413 
  L1CAM MUTATED L1CAM WILD-TYPE 
              1               6 
$`L1CAM MUTATED`
TCGA-EJ-7791 TCGA-EJ-A8FN TCGA-J4-A67O TCGA-KK-A59V TCGA-YL-A8SH TCGA-YL-A8SR 
       19.59        10.82        27.58       113.10        28.77         8.98 

$`L1CAM WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        4.21         6.48         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       56.52        41.46        45.14        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
      114.38        71.34        62.79        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37         3.09        14.53        13.28        10.13 

  L1CAM MUTATED L1CAM WILD-TYPE 
           8.98            0.72 
  L1CAM MUTATED L1CAM WILD-TYPE 
         113.10          165.17 
  L1CAM MUTATED L1CAM WILD-TYPE 
         23.585          27.290 
[1] "9.0 - 113.1 (23.6)" "0.7 - 165.2 (27.3)"
[1] "hr=" "21" 
D39V2, continuous
                 vv
clus               T2  T3  T4
  L1CAM MUTATED     3   3   0
  L1CAM WILD-TYPE 169 236   6
D39V3, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  T2             3             169
  T3             3             236
  T4             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"
D39V4, binary
                 cls
clus                0   1
  L1CAM MUTATED     6   0
  L1CAM WILD-TYPE 293  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      6    0
  L1CAM WILD-TYPE  293   58
   clus
vv  L1CAM MUTATED L1CAM WILD-TYPE
  0             6             293
  1             0              58
[1] 2 2
[1] FALSE
D39V5, binary
                 cls
clus                0   1
  L1CAM MUTATED     0   6
  L1CAM WILD-TYPE  15 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  L1CAM MUTATED      0    6
  L1CAM WILD-TYPE   15  399
                                        clus
vv                                       L1CAM MUTATED L1CAM WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             399
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  L1CAM MUTATED     5   1   0   0
  L1CAM WILD-TYPE 278 102   5  15
D39V6, multiclass
    clus
vv   L1CAM MUTATED L1CAM WILD-TYPE
  R0             5             278
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, continuous
D39V8, continuous
D39V9, continuous
D39V10, continuous
D39V11, continuous
D39V12, continuous
D39V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  L1CAM MUTATED       0                         0     1
  L1CAM WILD-TYPE     2                         7   146
D39V14, multiclass
[1] "Remove cluster labels:" "L1CAM MUTATED"         
clus
  L1CAM MUTATED L1CAM WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"L1CAM WILD-TYPE" "L1CAM WILD-TYPE" "L1CAM WILD-TYPE" 

Clustering(40) Variable = FAM47C MUTATION ANALYSIS
D40V1, survival
                  sevent
clus2                0   1
  FAM47C MUTATED     9   0
  FAM47C WILD-TYPE 403   7
  FAM47C MUTATED FAM47C WILD-TYPE 
               9              410 
  FAM47C MUTATED FAM47C WILD-TYPE 
               0                7 
$`FAM47C MUTATED`
TCGA-EJ-5516 TCGA-EJ-8474 TCGA-G9-7519 TCGA-HC-7749 TCGA-HC-8259 TCGA-HC-A6HX 
       46.55        25.18        27.91         1.97         2.27         1.25 
TCGA-HI-7169 TCGA-J4-A67R TCGA-VP-A87B 
       88.24        29.92        85.18 

$`FAM47C WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 
       36.69        48.53        38.53        36.23        60.23        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       38.10        24.85        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 
       17.16        25.71        30.51        30.84        17.85        24.56 
TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 
       31.43        19.36        22.42        28.27        23.87         2.17 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HY TCGA-HC-A76W 
       17.42         2.33         3.48         1.45         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7170 
        4.93         9.53        25.48        18.84        78.61        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       16.54        27.58        32.05        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        41.42        44.91        25.78       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D 
       75.91       109.58        97.41        23.93        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  FAM47C MUTATED FAM47C WILD-TYPE 
            1.25             0.72 
  FAM47C MUTATED FAM47C WILD-TYPE 
           88.24           165.17 
  FAM47C MUTATED FAM47C WILD-TYPE 
           27.91            27.24 
[1] "1.2 - 88.2 (27.9)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9300000"
D40V2, continuous
                  vv
clus                T2  T3  T4
  FAM47C MUTATED     5   4   0
  FAM47C WILD-TYPE 167 235   6
D40V3, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  T2              5              167
  T3              4              235
  T4              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"
D40V4, binary
                  cls
clus                 0   1
  FAM47C MUTATED     7   0
  FAM47C WILD-TYPE 292  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      7    0
  FAM47C WILD-TYPE  292   58
   clus
vv  FAM47C MUTATED FAM47C WILD-TYPE
  0              7              292
  1              0               58
[1] 2 2
[1] FALSE
D40V5, binary
                  cls
clus                 0   1
  FAM47C MUTATED     0   9
  FAM47C WILD-TYPE  15 396
[1] "tbl2"
                  cls
clus               [,1] [,2]
  FAM47C MUTATED      0    9
  FAM47C WILD-TYPE   15  396
                                        clus
vv                                       FAM47C MUTATED FAM47C WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 9              396
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  FAM47C MUTATED     8   1   0   0
  FAM47C WILD-TYPE 275 102   5  15
D40V6, multiclass
    clus
vv   FAM47C MUTATED FAM47C WILD-TYPE
  R0              8              275
  R1              1              102
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, continuous
D40V8, continuous
D40V9, continuous
D40V10, continuous
D40V11, continuous
D40V12, continuous
D40V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM47C MUTATED       0                         0     3
  FAM47C WILD-TYPE     2                         7   144
D40V14, multiclass
                           clus
vv                          FAM47C MUTATED FAM47C WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = CR1L MUTATION ANALYSIS
D41V1, survival
                sevent
clus2              0   1
  CR1L MUTATED     5   0
  CR1L WILD-TYPE 407   7
  CR1L MUTATED CR1L WILD-TYPE 
             5            414 
  CR1L MUTATED CR1L WILD-TYPE 
             0              7 
$`CR1L MUTATED`
TCGA-CH-5740 TCGA-CH-5761 TCGA-EJ-5519 TCGA-M7-A724 TCGA-VN-A88I 
        1.02         0.92        64.50        29.23         8.84 

$`CR1L WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 
       25.35         2.99         6.97        22.06        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
       31.00         1.02         2.04        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 
       10.82         9.27         9.83         8.75         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A725 
       21.14        12.62        13.15        34.85        25.08        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  CR1L MUTATED CR1L WILD-TYPE 
          0.92           0.72 
  CR1L MUTATED CR1L WILD-TYPE 
         64.50         165.17 
  CR1L MUTATED CR1L WILD-TYPE 
          8.84          27.34 
[1] "0.9 - 64.5 (8.8)"   "0.7 - 165.2 (27.3)"
[1] "hr="     "3300000"
D41V2, continuous
                vv
clus              T2  T3  T4
  CR1L MUTATED     1   4   0
  CR1L WILD-TYPE 171 235   6
D41V3, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  T2            1            171
  T3            4            235
  T4            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"
D41V4, binary
                cls
clus               0   1
  CR1L MUTATED     4   1
  CR1L WILD-TYPE 295  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      4    1
  CR1L WILD-TYPE  295   57
   clus
vv  CR1L MUTATED CR1L WILD-TYPE
  0            4            295
  1            1             57
[1] 2 2
[1] FALSE
D41V5, binary
                cls
clus               0   1
  CR1L MUTATED     0   5
  CR1L WILD-TYPE  15 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  CR1L MUTATED      0    5
  CR1L WILD-TYPE   15  400
                                        clus
vv                                       CR1L MUTATED CR1L WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               5            400
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  CR1L MUTATED     4   1   0   0
  CR1L WILD-TYPE 279 102   5  15
D41V6, multiclass
    clus
vv   CR1L MUTATED CR1L WILD-TYPE
  R0            4            279
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, continuous
D41V8, continuous
D41V9, continuous
D41V10, continuous
D41V11, continuous
D41V12, continuous
D41V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CR1L MUTATED       0                         0     3
  CR1L WILD-TYPE     2                         7   144
D41V14, multiclass
                           clus
vv                          CR1L MUTATED CR1L WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                3            144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = FAM120B MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  FAM120B MUTATED     3   0
  FAM120B WILD-TYPE 409   7
  FAM120B MUTATED FAM120B WILD-TYPE 
                3               416 
  FAM120B MUTATED FAM120B WILD-TYPE 
                0                 7 
$`FAM120B MUTATED`
TCGA-EJ-7123 TCGA-EJ-7314 TCGA-G9-6366 
       74.10        37.81         3.32 

$`FAM120B WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7315 
       29.06        88.34        93.70        83.57        36.13        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       39.39        44.81        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  FAM120B MUTATED FAM120B WILD-TYPE 
             3.32              0.72 
  FAM120B MUTATED FAM120B WILD-TYPE 
            74.10            165.17 
  FAM120B MUTATED FAM120B WILD-TYPE 
            37.81             27.24 
[1] "3.3 - 74.1 (37.8)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D42V2, continuous
                   vv
clus                 T2  T3  T4
  FAM120B MUTATED     1   2   0
  FAM120B WILD-TYPE 171 237   6
D42V3, multiclass
    clus
vv   FAM120B MUTATED FAM120B WILD-TYPE
  T2               1               171
  T3               2               237
  T4               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"
D42V4, binary
                   cls
clus                  0   1
  FAM120B MUTATED     2   0
  FAM120B WILD-TYPE 297  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      2    0
  FAM120B WILD-TYPE  297   58
   clus
vv  FAM120B MUTATED FAM120B WILD-TYPE
  0               2               297
  1               0                58
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                  0   1
  FAM120B MUTATED     0   3
  FAM120B WILD-TYPE  15 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM120B MUTATED      0    3
  FAM120B WILD-TYPE   15  402
                                        clus
vv                                       FAM120B MUTATED FAM120B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  3               402
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  FAM120B MUTATED     3   0   0   0
  FAM120B WILD-TYPE 280 103   5  15
D42V6, multiclass
    clus
vv   FAM120B MUTATED FAM120B WILD-TYPE
  R0               3               280
  R1               0               103
  R2               0                 5
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, continuous
[1] "Remove cluster labels:" "FAM120B MUTATED"       
clus
  FAM120B MUTATED FAM120B WILD-TYPE 
                2               340 
       TCGA-2A-A8VL        TCGA-2A-A8VT        TCGA-2A-A8VV        TCGA-2A-A8VX 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-2A-A8W1        TCGA-2A-A8W3        TCGA-CH-5737        TCGA-CH-5739 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5740        TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5745        TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5751        TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5761        TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5765        TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5769        TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5789        TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-CH-5794        TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5497        TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5502        TCGA-EJ-5503        TCGA-EJ-5504        TCGA-EJ-5505 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508        TCGA-EJ-5509 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512        TCGA-EJ-5514 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517        TCGA-EJ-5518 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522        TCGA-EJ-5524 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527        TCGA-EJ-5530 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542        TCGA-EJ-7115 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7125        TCGA-EJ-7218        TCGA-EJ-7312        TCGA-EJ-7315 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7325        TCGA-EJ-7327 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-EJ-7797        TCGA-EJ-8468 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-8469        TCGA-EJ-8470        TCGA-EJ-8472        TCGA-EJ-8474 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A46B        TCGA-EJ-A46D        TCGA-EJ-A46E        TCGA-EJ-A46F 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A46G        TCGA-EJ-A65B        TCGA-EJ-A65D        TCGA-EJ-A65E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A65F        TCGA-EJ-A65G        TCGA-EJ-A65J        TCGA-EJ-A65M 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A6RA        TCGA-EJ-A6RC        TCGA-EJ-A7NF        TCGA-EJ-A7NG 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A7NJ        TCGA-EJ-A7NK        TCGA-EJ-A7NM        TCGA-EJ-A7NN 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A8FN        TCGA-EJ-A8FO        TCGA-EJ-A8FP        TCGA-EJ-A8FS 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-EJ-A8FU        TCGA-FC-7708        TCGA-FC-7961        TCGA-FC-A5OB 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-FC-A66V        TCGA-FC-A6HD        TCGA-FC-A8O0        TCGA-G9-6332 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6339 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6348        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6367 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6377        TCGA-G9-6379 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-7510        TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-G9-7525        TCGA-H9-A6BY        TCGA-HC-7078        TCGA-HC-7079 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230        TCGA-HC-7233 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7736        TCGA-HC-7737        TCGA-HC-7740        TCGA-HC-7742 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-7821        TCGA-HC-8216        TCGA-HC-8257        TCGA-HC-8258 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-8260        TCGA-HC-8262        TCGA-HC-8264        TCGA-HC-8265 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-8266        TCGA-HC-A48F        TCGA-HC-A4ZV        TCGA-HC-A631 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-A632        TCGA-HC-A6AL        TCGA-HC-A6AN        TCGA-HC-A6AS 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-A6HX        TCGA-HC-A76W        TCGA-HC-A76X        TCGA-HC-A8CY 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HC-A8D0        TCGA-HC-A8D1        TCGA-HI-7168        TCGA-HI-7169 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171        TCGA-J4-8200        TCGA-J4-A67L 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-A67M        TCGA-J4-A67N        TCGA-J4-A67O        TCGA-J4-A67R 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-A67S        TCGA-J4-A6G1        TCGA-J4-A6G3        TCGA-J4-A83I 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J4-A83J        TCGA-J4-A83L        TCGA-J4-A83M        TCGA-J9-A52B 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-J9-A52E        TCGA-J9-A8CM        TCGA-KC-A4BL        TCGA-KC-A4BN 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A4BO        TCGA-KC-A4BR        TCGA-KC-A4BV        TCGA-KC-A7F3 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A7F5        TCGA-KC-A7F6        TCGA-KC-A7FA        TCGA-KC-A7FD 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KC-A7FE        TCGA-KK-A59V        TCGA-KK-A59X        TCGA-KK-A59Y 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A59Z        TCGA-KK-A5A1        TCGA-KK-A6DY        TCGA-KK-A6E0 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A6E1        TCGA-KK-A6E2        TCGA-KK-A6E3        TCGA-KK-A6E4 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A6E5        TCGA-KK-A6E6        TCGA-KK-A6E7        TCGA-KK-A6E8 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A7AP        TCGA-KK-A7AQ        TCGA-KK-A7AU        TCGA-KK-A7AV 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A7AW        TCGA-KK-A7AY        TCGA-KK-A7AZ        TCGA-KK-A7B0 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A7B1        TCGA-KK-A7B2        TCGA-KK-A7B3        TCGA-KK-A7B4 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A8I4        TCGA-KK-A8I6        TCGA-KK-A8I7        TCGA-KK-A8IA 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-KK-A8ID        TCGA-KK-A8IJ        TCGA-KK-A8IL        TCGA-M7-A71Z 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-M7-A722        TCGA-M7-A723        TCGA-M7-A724        TCGA-M7-A725 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-QU-A6IL        TCGA-QU-A6IM        TCGA-QU-A6IN        TCGA-QU-A6IO 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-QU-A6IP        TCGA-SU-A7E7        TCGA-V1-A8MF        TCGA-V1-A8MJ 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-V1-A8ML        TCGA-V1-A8MM        TCGA-V1-A8MU        TCGA-V1-A8WL 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-V1-A8WV        TCGA-V1-A8X3        TCGA-VN-A88I        TCGA-VN-A88K 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-VN-A88L        TCGA-VN-A88M        TCGA-VN-A88N        TCGA-VN-A88O 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-VN-A88P        TCGA-VN-A88Q        TCGA-VN-A88R        TCGA-VP-A872 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-VP-A875        TCGA-VP-A876        TCGA-VP-A878        TCGA-VP-A879 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-VP-A87B        TCGA-VP-A87C        TCGA-VP-A87D        TCGA-VP-A87E 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-VP-A87H        TCGA-VP-A87J        TCGA-VP-A87K        TCGA-WW-A8ZI 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-X4-A8KQ        TCGA-XA-A8JR        TCGA-XJ-A83F        TCGA-XJ-A83G 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-XJ-A9DI        TCGA-XJ-A9DX        TCGA-Y6-A8TL        TCGA-YJ-A8SW 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-YL-A8HK        TCGA-YL-A8HL        TCGA-YL-A8HM        TCGA-YL-A8HO 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-YL-A8S8        TCGA-YL-A8S9        TCGA-YL-A8SA        TCGA-YL-A8SB 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-YL-A8SC        TCGA-YL-A8SF        TCGA-YL-A8SH        TCGA-YL-A8SJ 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-YL-A8SK        TCGA-YL-A8SL        TCGA-YL-A8SQ        TCGA-YL-A8SR 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-YL-A9WH        TCGA-YL-A9WI        TCGA-YL-A9WJ        TCGA-YL-A9WK 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
       TCGA-ZG-A8QW        TCGA-ZG-A8QX        TCGA-ZG-A8QY        TCGA-ZG-A8QZ 
"FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" "FAM120B WILD-TYPE" 
D42V8, continuous
D42V9, continuous
D42V10, continuous
D42V11, continuous
D42V12, continuous
D42V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM120B MUTATED       0                         0     3
  FAM120B WILD-TYPE     2                         7   144
D42V14, multiclass
                           clus
vv                          FAM120B MUTATED FAM120B WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 7
  WHITE                                   3               144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = EDC4 MUTATION ANALYSIS
D43V1, survival
                sevent
clus2              0   1
  EDC4 MUTATED     3   0
  EDC4 WILD-TYPE 409   7
  EDC4 MUTATED EDC4 WILD-TYPE 
             3            416 
  EDC4 MUTATED EDC4 WILD-TYPE 
             0              7 
$`EDC4 MUTATED`
TCGA-EJ-7315 TCGA-HC-7078 TCGA-HC-7737 
       33.14        65.26         2.10 

$`EDC4 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       37.81        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7738 
        1.68         2.37        38.17        44.55         0.72        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  EDC4 MUTATED EDC4 WILD-TYPE 
          2.10           0.72 
  EDC4 MUTATED EDC4 WILD-TYPE 
         65.26         165.17 
  EDC4 MUTATED EDC4 WILD-TYPE 
         33.14          27.24 
[1] "2.1 - 65.3 (33.1)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D43V2, continuous
                vv
clus              T2  T3  T4
  EDC4 MUTATED     1   2   0
  EDC4 WILD-TYPE 171 237   6
D43V3, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  T2            1            171
  T3            2            237
  T4            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"
D43V4, binary
                cls
clus               0   1
  EDC4 MUTATED     2   1
  EDC4 WILD-TYPE 297  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      2    1
  EDC4 WILD-TYPE  297   57
   clus
vv  EDC4 MUTATED EDC4 WILD-TYPE
  0            2            297
  1            1             57
[1] 2 2
[1] FALSE
D43V5, binary
                cls
clus               0   1
  EDC4 MUTATED     0   3
  EDC4 WILD-TYPE  15 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  EDC4 MUTATED      0    3
  EDC4 WILD-TYPE   15  402
                                        clus
vv                                       EDC4 MUTATED EDC4 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  EDC4 MUTATED     3   0   0   0
  EDC4 WILD-TYPE 280 103   5  15
D43V6, multiclass
    clus
vv   EDC4 MUTATED EDC4 WILD-TYPE
  R0            3            280
  R1            0            103
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, continuous
D43V8, continuous
D43V9, continuous
D43V10, continuous
D43V11, continuous
D43V12, continuous
D43V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EDC4 MUTATED       0                         1     2
  EDC4 WILD-TYPE     2                         6   145
D43V14, multiclass
                           clus
vv                          EDC4 MUTATED EDC4 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            1              6
  WHITE                                2            145
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = KIRREL MUTATION ANALYSIS
D44V1, survival
                  sevent
clus2                0   1
  KIRREL MUTATED     5   0
  KIRREL WILD-TYPE 407   7
  KIRREL MUTATED KIRREL WILD-TYPE 
               5              414 
  KIRREL MUTATED KIRREL WILD-TYPE 
               0                7 
$`KIRREL MUTATED`
TCGA-EJ-5515 TCGA-EJ-5519 TCGA-G9-6353 TCGA-HC-8262 TCGA-KK-A7AQ 
       60.23        64.50        50.70        22.32        52.93 

$`KIRREL WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5516 TCGA-EJ-5517 
       36.69        48.53        38.53        36.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       52.27        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8264 TCGA-HC-8265 
        2.17         2.27        22.55        17.95         1.58        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 
       29.92        27.39         6.02        25.28        27.91        16.83 
TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N 
       22.52        22.88        10.78        23.67        14.37        20.28 
TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM 
       13.87         5.85         6.97        10.62        13.32        15.22 
TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR 
       40.67        12.69        30.71        59.67        19.96        44.35 
TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD 
       43.66        21.86         2.99         8.65        19.66         8.88 
TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
       11.57       113.10        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AU 
       49.25       113.33        67.07        58.19         6.44        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  KIRREL MUTATED KIRREL WILD-TYPE 
           22.32             0.72 
  KIRREL MUTATED KIRREL WILD-TYPE 
           64.50           165.17 
  KIRREL MUTATED KIRREL WILD-TYPE 
          52.930           27.175 
[1] "22.3 - 64.5 (52.9)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9200000"
D44V2, continuous
                  vv
clus                T2  T3  T4
  KIRREL MUTATED     2   3   0
  KIRREL WILD-TYPE 170 236   6
D44V3, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  T2              2              170
  T3              3              236
  T4              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"
D44V4, binary
                  cls
clus                 0   1
  KIRREL MUTATED     3   1
  KIRREL WILD-TYPE 296  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      3    1
  KIRREL WILD-TYPE  296   57
   clus
vv  KIRREL MUTATED KIRREL WILD-TYPE
  0              3              296
  1              1               57
[1] 2 2
[1] FALSE
D44V5, binary
                  cls
clus                 0   1
  KIRREL MUTATED     0   5
  KIRREL WILD-TYPE  15 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  KIRREL MUTATED      0    5
  KIRREL WILD-TYPE   15  400
                                        clus
vv                                       KIRREL MUTATED KIRREL WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              400
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  KIRREL MUTATED     4   1   0   0
  KIRREL WILD-TYPE 279 102   5  15
D44V6, multiclass
    clus
vv   KIRREL MUTATED KIRREL WILD-TYPE
  R0              4              279
  R1              1              102
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, continuous
D44V8, continuous
D44V9, continuous
D44V10, continuous
D44V11, continuous
D44V12, continuous
D44V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIRREL MUTATED       0                         0     3
  KIRREL WILD-TYPE     2                         7   144
D44V14, multiclass
                           clus
vv                          KIRREL MUTATED KIRREL WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  3              144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = TCERG1 MUTATION ANALYSIS
D45V1, survival
                  sevent
clus2                0   1
  TCERG1 MUTATED     4   0
  TCERG1 WILD-TYPE 408   7
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               4              415 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               0                7 
$`TCERG1 MUTATED`
TCGA-G9-6336 TCGA-HC-7749 TCGA-KK-A8I5 TCGA-VP-A872 
       67.99         1.97       101.79       111.39 

$`TCERG1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       24.59        26.04        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
       67.99        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A875 TCGA-VP-A876 
       15.81        41.42        44.91        25.78        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  TCERG1 MUTATED TCERG1 WILD-TYPE 
            1.97             0.72 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
          111.39           165.17 
  TCERG1 MUTATED TCERG1 WILD-TYPE 
           84.89            27.19 
[1] "2.0 - 111.4 (84.9)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9400000"
D45V2, continuous
                  vv
clus                T2  T3  T4
  TCERG1 MUTATED     1   2   0
  TCERG1 WILD-TYPE 171 237   6
D45V3, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  T2              1              171
  T3              2              237
  T4              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"
D45V4, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     4   0
  TCERG1 WILD-TYPE 295  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      4    0
  TCERG1 WILD-TYPE  295   58
   clus
vv  TCERG1 MUTATED TCERG1 WILD-TYPE
  0              4              295
  1              0               58
[1] 2 2
[1] FALSE
D45V5, binary
                  cls
clus                 0   1
  TCERG1 MUTATED     1   3
  TCERG1 WILD-TYPE  14 402
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCERG1 MUTATED      1    3
  TCERG1 WILD-TYPE   14  402
                                        clus
vv                                       TCERG1 MUTATED TCERG1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              1               14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 3              402
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  TCERG1 MUTATED     3   1   0   0
  TCERG1 WILD-TYPE 280 102   5  15
D45V6, multiclass
    clus
vv   TCERG1 MUTATED TCERG1 WILD-TYPE
  R0              3              280
  R1              1              102
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, continuous
D45V8, continuous
D45V9, continuous
D45V10, continuous
D45V11, continuous
D45V12, continuous
D45V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TCERG1 MUTATED       0                         0     2
  TCERG1 WILD-TYPE     2                         7   145
D45V14, multiclass
[1] "Remove cluster labels:" "TCERG1 MUTATED"        
clus
  TCERG1 MUTATED TCERG1 WILD-TYPE 
               2              154 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-EJ-7797       TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6333       TCGA-G9-6338       TCGA-G9-6342 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351       TCGA-G9-6353 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362       TCGA-G9-6363 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366       TCGA-G9-6367 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371       TCGA-G9-6373 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384       TCGA-G9-6385 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499       TCGA-H9-7775 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078       TCGA-HC-7079 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209       TCGA-HC-7210 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7211       TCGA-HC-7212       TCGA-HC-7213       TCGA-HC-7230 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818       TCGA-HC-7819 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168       TCGA-HI-7169 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 
      TCGA-HI-7170       TCGA-HI-7171 
"TCERG1 WILD-TYPE" "TCERG1 WILD-TYPE" 

Clustering(46) Variable = SLC16A6 MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  SLC16A6 MUTATED     4   0
  SLC16A6 WILD-TYPE 408   7
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                4               415 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                0                 7 
$`SLC16A6 MUTATED`
TCGA-G9-6498 TCGA-HC-7212 TCGA-KK-A59Y TCGA-YL-A8SL 
       64.18        28.60        44.68        32.45 

$`SLC16A6 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 
       58.45        25.15        27.29        58.22        56.75        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 
       36.36        37.35        14.47        28.54         0.79        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Z 
       19.66         8.88        11.57       113.10        56.28        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       46.29       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
            28.60              0.72 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
            64.18            165.17 
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
           38.565            27.160 
[1] "28.6 - 64.2 (38.6)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D46V2, continuous
                   vv
clus                 T2  T3  T4
  SLC16A6 MUTATED     1   3   0
  SLC16A6 WILD-TYPE 171 236   6
D46V3, multiclass
    clus
vv   SLC16A6 MUTATED SLC16A6 WILD-TYPE
  T2               1               171
  T3               3               236
  T4               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"
D46V4, binary
                   cls
clus                  0   1
  SLC16A6 MUTATED     1   2
  SLC16A6 WILD-TYPE 298  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A6 MUTATED      1    2
  SLC16A6 WILD-TYPE  298   56
   clus
vv  SLC16A6 MUTATED SLC16A6 WILD-TYPE
  0               1               298
  1               2                56
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                  0   1
  SLC16A6 MUTATED     0   4
  SLC16A6 WILD-TYPE  15 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SLC16A6 MUTATED      0    4
  SLC16A6 WILD-TYPE   15  401
                                        clus
vv                                       SLC16A6 MUTATED SLC16A6 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  4               401
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  SLC16A6 MUTATED     1   1   0   1
  SLC16A6 WILD-TYPE 282 102   5  14
D46V6, multiclass
    clus
vv   SLC16A6 MUTATED SLC16A6 WILD-TYPE
  R0               1               282
  R1               1               102
  R2               0                 5
  RX               1                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, continuous
D46V8, continuous
D46V9, continuous
D46V10, continuous
D46V11, continuous
D46V12, continuous
D46V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SLC16A6 MUTATED       0                         0     1
  SLC16A6 WILD-TYPE     2                         7   146
D46V14, multiclass
[1] "Remove cluster labels:" "SLC16A6 MUTATED"       
clus
  SLC16A6 MUTATED SLC16A6 WILD-TYPE 
                1               155 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7327        TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7781        TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7785        TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7791        TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-EJ-7797        TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7213        TCGA-HC-7230 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" "SLC16A6 WILD-TYPE" 

Clustering(47) Variable = NKX3-1 MUTATION ANALYSIS
D47V1, survival
                  sevent
clus2                0   1
  NKX3-1 MUTATED     5   0
  NKX3-1 WILD-TYPE 407   7
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               5              414 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
               0                7 
$`NKX3-1 MUTATED`
TCGA-CH-5745 TCGA-CH-5767 TCGA-CH-5794 TCGA-EJ-5517 TCGA-EJ-5530 
        2.99        15.06        29.00        47.80        60.23 

$`NKX3-1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
        1.02        23.01         1.02        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       27.16        33.11        19.56        13.32        29.79        46.52 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       44.88        26.30        45.73        28.93        30.31        27.19 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
       23.90        38.93        48.13        36.69        48.53        38.53 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       36.23        60.23        46.55        52.27        64.50        51.88 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 
       68.35        43.07        36.66        38.76        39.75        41.85 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 
       47.87        29.06        88.34        74.10        93.70        83.57 
TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 
       36.13        37.81        33.14        25.35        33.83        27.09 
TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
       35.18        30.35        27.68         6.28        24.39        23.90 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
       38.37        25.87        25.68        20.55        14.53        14.14 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 
       18.15        19.59        17.29         3.75        23.05        19.92 
TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B 
       77.16        76.41        38.10        24.85        25.18        21.60 
TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I 
       20.58        17.23        25.74        21.96        23.80        21.96 
TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J 
       23.34        12.92        13.71        18.41        21.90        14.83 
TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH 
        7.56        11.61        28.70         8.22        14.20        15.58 
TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO 
        6.48        15.65         4.21         6.48        10.82         9.27 
TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI 
        9.83         8.75         4.54        28.41        15.42        13.45 
TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 
       22.36        17.23        16.24         1.78        41.62        87.35 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 
       81.04        67.99        66.67        83.87        55.76        18.21 
TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 
       68.68        49.81        46.16        50.70        49.35        47.15 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       46.52        47.44        45.30        39.39        44.81         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 
       40.18        39.95        38.01        40.31        26.66        31.50 
TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       37.97        58.45        25.15        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       64.18        50.73        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       28.18        32.68         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
            2.99             0.72 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
           60.23           165.17 
  NKX3-1 MUTATED NKX3-1 WILD-TYPE 
           29.00            27.24 
[1] "3.0 - 60.2 (29.0)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D47V2, continuous
                  vv
clus                T2  T3  T4
  NKX3-1 MUTATED     4   1   0
  NKX3-1 WILD-TYPE 168 238   6
D47V3, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  T2              4              168
  T3              1              238
  T4              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"
D47V4, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     5   0
  NKX3-1 WILD-TYPE 294  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      5    0
  NKX3-1 WILD-TYPE  294   58
   clus
vv  NKX3-1 MUTATED NKX3-1 WILD-TYPE
  0              5              294
  1              0               58
[1] 2 2
[1] FALSE
D47V5, binary
                  cls
clus                 0   1
  NKX3-1 MUTATED     0   5
  NKX3-1 WILD-TYPE  15 400
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NKX3-1 MUTATED      0    5
  NKX3-1 WILD-TYPE   15  400
                                        clus
vv                                       NKX3-1 MUTATED NKX3-1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 5              400
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  NKX3-1 MUTATED     5   0   0   0
  NKX3-1 WILD-TYPE 278 103   5  15
D47V6, multiclass
    clus
vv   NKX3-1 MUTATED NKX3-1 WILD-TYPE
  R0              5              278
  R1              0              103
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, continuous
D47V8, continuous
D47V9, continuous
D47V10, continuous
D47V11, continuous
D47V12, continuous
D47V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NKX3-1 MUTATED       0                         0     5
  NKX3-1 WILD-TYPE     2                         7   142
D47V14, multiclass
                           clus
vv                          NKX3-1 MUTATED NKX3-1 WILD-TYPE
  ASIAN                                  0                2
  BLACK OR AFRICAN AMERICAN              0                7
  WHITE                                  5              142
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = RNF17 MUTATION ANALYSIS
D48V1, survival
                 sevent
clus2               0   1
  RNF17 MUTATED     3   0
  RNF17 WILD-TYPE 409   7
  RNF17 MUTATED RNF17 WILD-TYPE 
              3             416 
  RNF17 MUTATED RNF17 WILD-TYPE 
              0               7 
$`RNF17 MUTATED`
TCGA-CH-5739 TCGA-CH-5740 TCGA-EJ-5516 
       22.06         1.02        46.55 

$`RNF17 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
       25.35         2.99         6.97        12.99        13.97         1.97 
TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        2.99        24.03         1.02        13.02        35.01        31.00 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       38.53        36.23        60.23        47.80        52.27        64.50 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       51.88        68.35        43.07        36.66        38.76        39.75 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       60.23        41.85        47.87        29.06        88.34        74.10 
TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       93.70        83.57        36.13        37.81        33.14        25.35 
TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
       33.83        27.09        35.18        30.35        27.68         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
       24.39        23.90        38.37        25.87        25.68        20.55 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 
       14.53        14.14        18.15        19.59        17.29         3.75 
TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 
       23.05        19.92        77.16        76.41        38.10        24.85 
TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G 
       25.18        21.60        20.58        17.23        25.74        21.96 
TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F 
       23.80        21.96        23.34        12.92        13.71        18.41 
TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF 
       21.90        14.83         7.56        11.61        28.70         8.22 
TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN 
       14.20        15.58         6.48        15.65         4.21         6.48 
TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 
       10.82         9.27         9.83         8.75         4.54        28.41 
TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
       15.42        13.45        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 
       26.66        31.50        37.97        58.45        25.15        27.29 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 
       58.22        56.75        64.18        50.73        38.96        27.91 
TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX 
       30.97        35.34        28.18        32.68         6.08        30.94 
TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 
        3.68        19.76        65.26         2.93        36.36        37.35 
TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 
       14.47        28.54         0.79        28.60        40.08         1.68 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  RNF17 MUTATED RNF17 WILD-TYPE 
           1.02            0.72 
  RNF17 MUTATED RNF17 WILD-TYPE 
          46.55          165.17 
  RNF17 MUTATED RNF17 WILD-TYPE 
          22.06           27.34 
[1] "1.0 - 46.5 (22.1)"  "0.7 - 165.2 (27.3)"
[1] "hr="     "3300000"
D48V2, continuous
                 vv
clus               T2  T3  T4
  RNF17 MUTATED     1   2   0
  RNF17 WILD-TYPE 171 237   6
D48V3, multiclass
    clus
vv   RNF17 MUTATED RNF17 WILD-TYPE
  T2             1             171
  T3             2             237
  T4             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"
D48V4, binary
                 cls
clus                0   1
  RNF17 MUTATED     3   0
  RNF17 WILD-TYPE 296  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF17 MUTATED      3    0
  RNF17 WILD-TYPE  296   58
   clus
vv  RNF17 MUTATED RNF17 WILD-TYPE
  0             3             296
  1             0              58
[1] 2 2
[1] FALSE
D48V5, binary
                 cls
clus                0   1
  RNF17 MUTATED     0   3
  RNF17 WILD-TYPE  15 402
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RNF17 MUTATED      0    3
  RNF17 WILD-TYPE   15  402
                                        clus
vv                                       RNF17 MUTATED RNF17 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                3             402
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  RNF17 MUTATED     3   0   0   0
  RNF17 WILD-TYPE 280 103   5  15
D48V6, multiclass
    clus
vv   RNF17 MUTATED RNF17 WILD-TYPE
  R0             3             280
  R1             0             103
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, continuous
D48V8, continuous
D48V9, continuous
D48V10, continuous
D48V11, continuous
D48V12, continuous
[1] "Remove cluster labels:" "RNF17 MUTATED"         
clus
  RNF17 MUTATED RNF17 WILD-TYPE 
              2             416 
     TCGA-2A-A8VL      TCGA-2A-A8VO      TCGA-2A-A8VT      TCGA-2A-A8VV 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-2A-A8VX      TCGA-2A-A8W1      TCGA-2A-A8W3      TCGA-CH-5737 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5738      TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5745      TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5751      TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5761      TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5765      TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5502      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7125      TCGA-EJ-7218      TCGA-EJ-7312      TCGA-EJ-7314 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7318      TCGA-EJ-7321 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7325      TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786      TCGA-EJ-7788 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792      TCGA-EJ-7793 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-7794      TCGA-EJ-7797      TCGA-EJ-8468      TCGA-EJ-8469 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-8470      TCGA-EJ-8472      TCGA-EJ-8474      TCGA-EJ-A46B 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A46D      TCGA-EJ-A46E      TCGA-EJ-A46F      TCGA-EJ-A46G 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A46H      TCGA-EJ-A46I      TCGA-EJ-A65B      TCGA-EJ-A65D 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A65E      TCGA-EJ-A65F      TCGA-EJ-A65G      TCGA-EJ-A65J 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A65M      TCGA-EJ-A6RA      TCGA-EJ-A6RC      TCGA-EJ-A7NF 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A7NG      TCGA-EJ-A7NH      TCGA-EJ-A7NJ      TCGA-EJ-A7NK 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A7NM      TCGA-EJ-A7NN      TCGA-EJ-A8FN      TCGA-EJ-A8FO 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-EJ-A8FP      TCGA-EJ-A8FS      TCGA-EJ-A8FU      TCGA-FC-7708 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-FC-7961      TCGA-FC-A4JI      TCGA-FC-A5OB      TCGA-FC-A66V 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-FC-A6HD      TCGA-FC-A8O0      TCGA-G9-6329      TCGA-G9-6332 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6339 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6342      TCGA-G9-6343      TCGA-G9-6347      TCGA-G9-6348 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6354      TCGA-G9-6356 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6365 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369      TCGA-G9-6370 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377      TCGA-G9-6378 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6379      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6498      TCGA-G9-6499      TCGA-G9-7510 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-7519      TCGA-G9-7521      TCGA-G9-7522      TCGA-G9-7523 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-G9-7525      TCGA-H9-7775      TCGA-H9-A6BX      TCGA-H9-A6BY 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7817 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-7818      TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8213      TCGA-HC-8216      TCGA-HC-8256      TCGA-HC-8257 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8258      TCGA-HC-8259      TCGA-HC-8260      TCGA-HC-8261 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-8262      TCGA-HC-8264      TCGA-HC-8265      TCGA-HC-8266 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A48F      TCGA-HC-A4ZV      TCGA-HC-A631      TCGA-HC-A632 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A6AL      TCGA-HC-A6AN      TCGA-HC-A6AO      TCGA-HC-A6AP 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A6AQ      TCGA-HC-A6AS      TCGA-HC-A6HX      TCGA-HC-A6HY 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A76W      TCGA-HC-A76X      TCGA-HC-A8CY      TCGA-HC-A8D0 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HC-A8D1      TCGA-HI-7168      TCGA-HI-7169      TCGA-HI-7170 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-HI-7171      TCGA-J4-8198      TCGA-J4-8200      TCGA-J4-A67K 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A67L      TCGA-J4-A67M      TCGA-J4-A67N      TCGA-J4-A67O 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A67Q      TCGA-J4-A67R      TCGA-J4-A67S      TCGA-J4-A67T 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A6G1      TCGA-J4-A6G3      TCGA-J4-A6M7      TCGA-J4-A83I 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A83J      TCGA-J4-A83K      TCGA-J4-A83L      TCGA-J4-A83M 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J4-A83N      TCGA-J9-A52B      TCGA-J9-A52C      TCGA-J9-A52D 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J9-A52E      TCGA-J9-A8CL      TCGA-J9-A8CM      TCGA-J9-A8CN 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-J9-A8CP      TCGA-KC-A4BL      TCGA-KC-A4BN      TCGA-KC-A4BO 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KC-A4BR      TCGA-KC-A4BV      TCGA-KC-A7F3      TCGA-KC-A7F5 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KC-A7F6      TCGA-KC-A7FA      TCGA-KC-A7FD      TCGA-KC-A7FE 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A59V      TCGA-KK-A59X      TCGA-KK-A59Y      TCGA-KK-A59Z 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A5A1      TCGA-KK-A6DY      TCGA-KK-A6E0      TCGA-KK-A6E1 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A6E2      TCGA-KK-A6E3      TCGA-KK-A6E4      TCGA-KK-A6E5 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A6E6      TCGA-KK-A6E7      TCGA-KK-A6E8      TCGA-KK-A7AP 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A7AQ      TCGA-KK-A7AU      TCGA-KK-A7AV      TCGA-KK-A7AW 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A7AY      TCGA-KK-A7AZ      TCGA-KK-A7B0      TCGA-KK-A7B1 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A7B2      TCGA-KK-A7B3      TCGA-KK-A7B4      TCGA-KK-A8I4 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A8I5      TCGA-KK-A8I6      TCGA-KK-A8I7      TCGA-KK-A8I8 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A8I9      TCGA-KK-A8IA      TCGA-KK-A8IB      TCGA-KK-A8IC 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A8ID      TCGA-KK-A8IF      TCGA-KK-A8IG      TCGA-KK-A8IH 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A8II      TCGA-KK-A8IJ      TCGA-KK-A8IK      TCGA-KK-A8IL 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-KK-A8IM      TCGA-M7-A71Y      TCGA-M7-A71Z      TCGA-M7-A720 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-M7-A721      TCGA-M7-A722      TCGA-M7-A723      TCGA-M7-A724 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-M7-A725      TCGA-QU-A6IL      TCGA-QU-A6IM      TCGA-QU-A6IN 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-QU-A6IO      TCGA-QU-A6IP      TCGA-SU-A7E7      TCGA-V1-A8MF 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-V1-A8MG      TCGA-V1-A8MJ      TCGA-V1-A8MK      TCGA-V1-A8ML 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-V1-A8MM      TCGA-V1-A8MU      TCGA-V1-A8WL      TCGA-V1-A8WN 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-V1-A8WS      TCGA-V1-A8WV      TCGA-V1-A8X3      TCGA-VN-A88I 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-VN-A88K      TCGA-VN-A88L      TCGA-VN-A88M      TCGA-VN-A88N 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-VN-A88O      TCGA-VN-A88P      TCGA-VN-A88Q      TCGA-VN-A88R 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-VP-A872      TCGA-VP-A875      TCGA-VP-A876      TCGA-VP-A878 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-VP-A879      TCGA-VP-A87B      TCGA-VP-A87C      TCGA-VP-A87D 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-VP-A87E      TCGA-VP-A87H      TCGA-VP-A87J      TCGA-VP-A87K 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-WW-A8ZI      TCGA-X4-A8KQ      TCGA-X4-A8KS      TCGA-XA-A8JR 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-XJ-A83F      TCGA-XJ-A83G      TCGA-XJ-A83H      TCGA-XJ-A9DI 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-XJ-A9DK      TCGA-XJ-A9DQ      TCGA-XJ-A9DX      TCGA-Y6-A8TL 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YJ-A8SW      TCGA-YL-A8HJ      TCGA-YL-A8HK      TCGA-YL-A8HL 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YL-A8HM      TCGA-YL-A8HO      TCGA-YL-A8S8      TCGA-YL-A8S9 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YL-A8SA      TCGA-YL-A8SB      TCGA-YL-A8SC      TCGA-YL-A8SF 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YL-A8SH      TCGA-YL-A8SJ      TCGA-YL-A8SK      TCGA-YL-A8SL 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YL-A8SO      TCGA-YL-A8SP      TCGA-YL-A8SQ      TCGA-YL-A8SR 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-YL-A9WH      TCGA-YL-A9WI      TCGA-YL-A9WJ      TCGA-YL-A9WK 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
     TCGA-ZG-A8QW      TCGA-ZG-A8QX      TCGA-ZG-A8QY      TCGA-ZG-A8QZ 
"RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" "RNF17 WILD-TYPE" 
D48V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RNF17 MUTATED       0                         0     3
  RNF17 WILD-TYPE     2                         7   144
D48V14, multiclass
                           clus
vv                          RNF17 MUTATED RNF17 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               7
  WHITE                                 3             144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = KYNU MUTATION ANALYSIS
D49V1, survival
                sevent
clus2              0   1
  KYNU MUTATED     3   0
  KYNU WILD-TYPE 409   7
  KYNU MUTATED KYNU WILD-TYPE 
             3            416 
  KYNU MUTATED KYNU WILD-TYPE 
             0              7 
$`KYNU MUTATED`
TCGA-EJ-5498 TCGA-EJ-5504 TCGA-VN-A88I 
       29.79        28.93         8.84 

$`KYNU WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5505 
       13.32        46.52        44.88        26.30        45.73        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
       22.55         6.64        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  KYNU MUTATED KYNU WILD-TYPE 
          8.84           0.72 
  KYNU MUTATED KYNU WILD-TYPE 
         29.79         165.17 
  KYNU MUTATED KYNU WILD-TYPE 
         28.93          27.24 
[1] "8.8 - 29.8 (28.9)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D49V2, continuous
                vv
clus              T2  T3  T4
  KYNU MUTATED     1   2   0
  KYNU WILD-TYPE 171 237   6
D49V3, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  T2            1            171
  T3            2            237
  T4            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"
D49V4, binary
                cls
clus               0   1
  KYNU MUTATED     2   1
  KYNU WILD-TYPE 297  57
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      2    1
  KYNU WILD-TYPE  297   57
   clus
vv  KYNU MUTATED KYNU WILD-TYPE
  0            2            297
  1            1             57
[1] 2 2
[1] FALSE
D49V5, binary
                cls
clus               0   1
  KYNU MUTATED     0   3
  KYNU WILD-TYPE  15 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  KYNU MUTATED      0    3
  KYNU WILD-TYPE   15  402
                                        clus
vv                                       KYNU MUTATED KYNU WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  KYNU MUTATED     2   1   0   0
  KYNU WILD-TYPE 281 102   5  15
D49V6, multiclass
    clus
vv   KYNU MUTATED KYNU WILD-TYPE
  R0            2            281
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, continuous
D49V8, continuous
D49V9, continuous
D49V10, continuous
D49V11, continuous
D49V12, continuous
D49V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KYNU MUTATED       0                         0     2
  KYNU WILD-TYPE     2                         7   145
D49V14, multiclass
[1] "Remove cluster labels:" "KYNU MUTATED"          
clus
  KYNU MUTATED KYNU WILD-TYPE 
             2            154 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503     TCGA-EJ-5505 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7314     TCGA-EJ-7315 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7317     TCGA-EJ-7321     TCGA-EJ-7327     TCGA-EJ-7328 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791     TCGA-EJ-7792 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797     TCGA-FC-7708 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332     TCGA-G9-6333 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342     TCGA-G9-6343 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353     TCGA-G9-6356 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367     TCGA-G9-6369 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373     TCGA-G9-6377 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385     TCGA-G9-6494 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775     TCGA-HC-7075 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079     TCGA-HC-7080 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210     TCGA-HC-7211 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230     TCGA-HC-7231 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742     TCGA-HC-7744 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818     TCGA-HC-7819 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168     TCGA-HI-7169 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" "KYNU WILD-TYPE" 
    TCGA-HI-7170     TCGA-HI-7171 
"KYNU WILD-TYPE" "KYNU WILD-TYPE" 

Clustering(50) Variable = LARP1 MUTATION ANALYSIS
D50V1, survival
                 sevent
clus2               0   1
  LARP1 MUTATED     4   0
  LARP1 WILD-TYPE 408   7
  LARP1 MUTATED LARP1 WILD-TYPE 
              4             415 
  LARP1 MUTATED LARP1 WILD-TYPE 
              0               7 
$`LARP1 MUTATED`
TCGA-EJ-5519 TCGA-EJ-5527 TCGA-HC-8258 TCGA-XJ-A83F 
       64.50        39.75         2.17        37.05 

$`LARP1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       47.80        52.27        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       38.76        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
       23.87         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
       32.19         3.91        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  LARP1 MUTATED LARP1 WILD-TYPE 
           2.17            0.72 
  LARP1 MUTATED LARP1 WILD-TYPE 
          64.50          165.17 
  LARP1 MUTATED LARP1 WILD-TYPE 
          38.40           27.19 
[1] "2.2 - 64.5 (38.4)"  "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D50V2, continuous
                 vv
clus               T2  T3  T4
  LARP1 MUTATED     1   3   0
  LARP1 WILD-TYPE 171 236   6
D50V3, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  T2             1             171
  T3             3             236
  T4             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"
D50V4, binary
                 cls
clus                0   1
  LARP1 MUTATED     3   1
  LARP1 WILD-TYPE 296  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      3    1
  LARP1 WILD-TYPE  296   57
   clus
vv  LARP1 MUTATED LARP1 WILD-TYPE
  0             3             296
  1             1              57
[1] 2 2
[1] FALSE
D50V5, binary
                 cls
clus                0   1
  LARP1 MUTATED     0   4
  LARP1 WILD-TYPE  15 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      0    4
  LARP1 WILD-TYPE   15  401
                                        clus
vv                                       LARP1 MUTATED LARP1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             401
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  LARP1 MUTATED     2   0   0   1
  LARP1 WILD-TYPE 281 103   5  14
D50V6, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  R0             2             281
  R1             0             103
  R2             0               5
  RX             1              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, continuous
D50V8, continuous
D50V9, continuous
D50V10, continuous
D50V11, continuous
D50V12, continuous
D50V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP1 MUTATED       0                         0     2
  LARP1 WILD-TYPE     2                         7   145
D50V14, multiclass
[1] "Remove cluster labels:" "LARP1 MUTATED"         
clus
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5521      TCGA-EJ-5522 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5530 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"LARP1 WILD-TYPE" "LARP1 WILD-TYPE" 

Clustering(51) Variable = CDK12 MUTATION ANALYSIS
D51V1, survival
                 sevent
clus2               0   1
  CDK12 MUTATED     8   0
  CDK12 WILD-TYPE 404   7
  CDK12 MUTATED CDK12 WILD-TYPE 
              8             411 
  CDK12 MUTATED CDK12 WILD-TYPE 
              0               7 
$`CDK12 MUTATED`
TCGA-EJ-7784 TCGA-EJ-A46G TCGA-HC-8261 TCGA-HC-8265 TCGA-HC-A6HX TCGA-KK-A59X 
       25.68        21.96        17.95        15.88         1.25        56.28 
TCGA-KK-A5A1 TCGA-KK-A8ID 
       77.72        69.27 

$`CDK12 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.87        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       25.74        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 
       23.87         2.17         2.27        22.55        22.32         1.58 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HY 
        1.61        17.42         2.33         3.48         1.45         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
      113.10        44.68        86.40       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8IF TCGA-KK-A8IG 
       32.91        63.48         2.73        67.43        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        41.42        44.91        25.78       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         2.99        31.99        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 
       52.96        49.02        51.45        48.72        71.77        62.14 
TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH 
       60.56        16.83        56.52        41.46        45.14        28.77 
TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ 
       45.86        46.29        32.45       114.38        71.34        62.79 
TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW 
        8.98        14.04        53.36        60.99        62.37         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  CDK12 MUTATED CDK12 WILD-TYPE 
           1.25            0.72 
  CDK12 MUTATED CDK12 WILD-TYPE 
          77.72          165.17 
  CDK12 MUTATED CDK12 WILD-TYPE 
          23.82           27.39 
[1] "1.2 - 77.7 (23.8)"  "0.7 - 165.2 (27.4)"
[1] "hr="     "9300000"
D51V2, continuous
                 vv
clus               T2  T3  T4
  CDK12 MUTATED     3   5   0
  CDK12 WILD-TYPE 169 234   6
D51V3, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  T2             3             169
  T3             5             234
  T4             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"
D51V4, binary
                 cls
clus                0   1
  CDK12 MUTATED     5   2
  CDK12 WILD-TYPE 294  56
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      5    2
  CDK12 WILD-TYPE  294   56
   clus
vv  CDK12 MUTATED CDK12 WILD-TYPE
  0             5             294
  1             2              56
[1] 2 2
[1] FALSE
D51V5, binary
                 cls
clus                0   1
  CDK12 MUTATED     1   7
  CDK12 WILD-TYPE  14 398
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDK12 MUTATED      1    7
  CDK12 WILD-TYPE   14  398
                                        clus
vv                                       CDK12 MUTATED CDK12 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             1              14
  PROSTATE ADENOCARCINOMA ACINAR TYPE                7             398
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  CDK12 MUTATED     4   4   0   0
  CDK12 WILD-TYPE 279  99   5  15
D51V6, multiclass
    clus
vv   CDK12 MUTATED CDK12 WILD-TYPE
  R0             4             279
  R1             4              99
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, continuous
D51V8, continuous
D51V9, continuous
D51V10, continuous
D51V11, continuous
D51V12, continuous
D51V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDK12 MUTATED       0                         0     1
  CDK12 WILD-TYPE     2                         7   146
D51V14, multiclass
[1] "Remove cluster labels:" "CDK12 MUTATED"         
clus
  CDK12 MUTATED CDK12 WILD-TYPE 
              1             155 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5530      TCGA-EJ-5531      TCGA-EJ-5532 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-5542      TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7314      TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7327      TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7781      TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7785 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7080      TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7211      TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7231      TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7737      TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7744      TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7749      TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HC-7819      TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 
     TCGA-HI-7169      TCGA-HI-7170      TCGA-HI-7171 
"CDK12 WILD-TYPE" "CDK12 WILD-TYPE" "CDK12 WILD-TYPE" 

Clustering(52) Variable = ACPT MUTATION ANALYSIS
D52V1, survival
                sevent
clus2              0   1
  ACPT MUTATED     3   0
  ACPT WILD-TYPE 409   7
  ACPT MUTATED ACPT WILD-TYPE 
             3            416 
  ACPT MUTATED ACPT WILD-TYPE 
             0              7 
$`ACPT MUTATED`
TCGA-EJ-7328 TCGA-KK-A8I6 TCGA-X4-A8KS 
       27.68        21.96        32.19 

$`ACPT WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       30.35         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       23.67        14.37        20.28        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        86.40        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94        67.99       101.79        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        41.42        44.91        25.78       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       45.47         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  ACPT MUTATED ACPT WILD-TYPE 
         21.96           0.72 
  ACPT MUTATED ACPT WILD-TYPE 
         32.19         165.17 
  ACPT MUTATED ACPT WILD-TYPE 
         27.68          27.24 
[1] "22.0 - 32.2 (27.7)" "0.7 - 165.2 (27.2)"
[1] "hr="     "3300000"
D52V2, continuous
                vv
clus              T2  T3  T4
  ACPT MUTATED     1   2   0
  ACPT WILD-TYPE 171 237   6
D52V3, multiclass
    clus
vv   ACPT MUTATED ACPT WILD-TYPE
  T2            1            171
  T3            2            237
  T4            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"
D52V4, binary
                cls
clus               0   1
  ACPT MUTATED     2   0
  ACPT WILD-TYPE 297  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPT MUTATED      2    0
  ACPT WILD-TYPE  297   58
   clus
vv  ACPT MUTATED ACPT WILD-TYPE
  0            2            297
  1            0             58
[1] 2 2
[1] FALSE
D52V5, binary
                cls
clus               0   1
  ACPT MUTATED     0   3
  ACPT WILD-TYPE  15 402
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACPT MUTATED      0    3
  ACPT WILD-TYPE   15  402
                                        clus
vv                                       ACPT MUTATED ACPT WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               3            402
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  ACPT MUTATED     2   0   0   1
  ACPT WILD-TYPE 281 103   5  14
D52V6, multiclass
    clus
vv   ACPT MUTATED ACPT WILD-TYPE
  R0            2            281
  R1            0            103
  R2            0              5
  RX            1             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, continuous
[1] "Remove cluster labels:" "ACPT MUTATED"          
clus
  ACPT MUTATED ACPT WILD-TYPE 
             2            340 
    TCGA-2A-A8VL     TCGA-2A-A8VT     TCGA-2A-A8VV     TCGA-2A-A8VX 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-2A-A8W1     TCGA-2A-A8W3     TCGA-CH-5737     TCGA-CH-5739 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5740     TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5745     TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5794     TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5502     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7218     TCGA-EJ-7312 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7325     TCGA-EJ-7327     TCGA-EJ-7330     TCGA-EJ-7331 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7794     TCGA-EJ-7797 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-8468     TCGA-EJ-8469     TCGA-EJ-8470     TCGA-EJ-8472 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-8474     TCGA-EJ-A46B     TCGA-EJ-A46D     TCGA-EJ-A46E 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A46F     TCGA-EJ-A46G     TCGA-EJ-A65B     TCGA-EJ-A65D 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A65E     TCGA-EJ-A65F     TCGA-EJ-A65G     TCGA-EJ-A65J 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A65M     TCGA-EJ-A6RA     TCGA-EJ-A6RC     TCGA-EJ-A7NF 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A7NG     TCGA-EJ-A7NJ     TCGA-EJ-A7NK     TCGA-EJ-A7NM 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A7NN     TCGA-EJ-A8FN     TCGA-EJ-A8FO     TCGA-EJ-A8FP 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A8FS     TCGA-EJ-A8FU     TCGA-FC-7708     TCGA-FC-7961 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-FC-A5OB     TCGA-FC-A66V     TCGA-FC-A6HD     TCGA-FC-A8O0 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6339     TCGA-G9-6348     TCGA-G9-6356     TCGA-G9-6361 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6362     TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6377 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6379     TCGA-G9-6384     TCGA-G9-6494     TCGA-G9-6496 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7521     TCGA-G9-7522 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-7523     TCGA-G9-7525     TCGA-H9-A6BY     TCGA-HC-7078 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7233     TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7742     TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7752     TCGA-HC-7818 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-8258     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8264 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-8265     TCGA-HC-8266     TCGA-HC-A48F     TCGA-HC-A4ZV 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-A631     TCGA-HC-A632     TCGA-HC-A6AL     TCGA-HC-A6AN 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-A6AS     TCGA-HC-A6HX     TCGA-HC-A76W     TCGA-HC-A76X 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-A8CY     TCGA-HC-A8D0     TCGA-HC-A8D1     TCGA-HI-7168 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171     TCGA-J4-8200 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A67L     TCGA-J4-A67M     TCGA-J4-A67N     TCGA-J4-A67O 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A67R     TCGA-J4-A67S     TCGA-J4-A6G1     TCGA-J4-A6G3 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A83I     TCGA-J4-A83J     TCGA-J4-A83L     TCGA-J4-A83M 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J9-A52B     TCGA-J9-A52E     TCGA-J9-A8CM     TCGA-KC-A4BL 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KC-A4BN     TCGA-KC-A4BO     TCGA-KC-A4BR     TCGA-KC-A4BV 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KC-A7F3     TCGA-KC-A7F5     TCGA-KC-A7F6     TCGA-KC-A7FA 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KC-A7FD     TCGA-KC-A7FE     TCGA-KK-A59V     TCGA-KK-A59X 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A59Y     TCGA-KK-A59Z     TCGA-KK-A5A1     TCGA-KK-A6DY 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6E0     TCGA-KK-A6E1     TCGA-KK-A6E2     TCGA-KK-A6E3 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6E4     TCGA-KK-A6E5     TCGA-KK-A6E6     TCGA-KK-A6E7 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6E8     TCGA-KK-A7AP     TCGA-KK-A7AQ     TCGA-KK-A7AU 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A7AV     TCGA-KK-A7AW     TCGA-KK-A7AY     TCGA-KK-A7AZ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A7B0     TCGA-KK-A7B1     TCGA-KK-A7B2     TCGA-KK-A7B3 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A7B4     TCGA-KK-A8I4     TCGA-KK-A8I7     TCGA-KK-A8IA 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A8ID     TCGA-KK-A8IJ     TCGA-KK-A8IL     TCGA-M7-A71Z 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-M7-A722     TCGA-M7-A723     TCGA-M7-A724     TCGA-M7-A725 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-QU-A6IL     TCGA-QU-A6IM     TCGA-QU-A6IN     TCGA-QU-A6IO 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-QU-A6IP     TCGA-SU-A7E7     TCGA-V1-A8MF     TCGA-V1-A8MJ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-V1-A8ML     TCGA-V1-A8MM     TCGA-V1-A8MU     TCGA-V1-A8WL 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-V1-A8WV     TCGA-V1-A8X3     TCGA-VN-A88I     TCGA-VN-A88K 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VN-A88L     TCGA-VN-A88M     TCGA-VN-A88N     TCGA-VN-A88O 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VN-A88P     TCGA-VN-A88Q     TCGA-VN-A88R     TCGA-VP-A872 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A875     TCGA-VP-A876     TCGA-VP-A878     TCGA-VP-A879 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A87B     TCGA-VP-A87C     TCGA-VP-A87D     TCGA-VP-A87E 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A87H     TCGA-VP-A87J     TCGA-VP-A87K     TCGA-WW-A8ZI 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-X4-A8KQ     TCGA-XA-A8JR     TCGA-XJ-A83F     TCGA-XJ-A83G 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-XJ-A9DI     TCGA-XJ-A9DX     TCGA-Y6-A8TL     TCGA-YJ-A8SW 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8HK     TCGA-YL-A8HL     TCGA-YL-A8HM     TCGA-YL-A8HO 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8S8     TCGA-YL-A8S9     TCGA-YL-A8SA     TCGA-YL-A8SB 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8SC     TCGA-YL-A8SF     TCGA-YL-A8SH     TCGA-YL-A8SJ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8SK     TCGA-YL-A8SL     TCGA-YL-A8SQ     TCGA-YL-A8SR 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A9WH     TCGA-YL-A9WI     TCGA-YL-A9WJ     TCGA-YL-A9WK 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-ZG-A8QW     TCGA-ZG-A8QX     TCGA-ZG-A8QY     TCGA-ZG-A8QZ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
D52V8, continuous
D52V9, continuous
D52V10, continuous
D52V11, continuous
D52V12, continuous
D52V13, continuous
[1] "Remove cluster labels:" "ACPT MUTATED"          
clus
  ACPT MUTATED ACPT WILD-TYPE 
             2            366 
    TCGA-2A-A8VL     TCGA-2A-A8VO     TCGA-2A-A8VT     TCGA-2A-A8VV 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-2A-A8VX     TCGA-2A-A8W1     TCGA-2A-A8W3     TCGA-CH-5737 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740     TCGA-CH-5741 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745     TCGA-CH-5746 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5750     TCGA-CH-5751     TCGA-CH-5752     TCGA-CH-5753 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5754     TCGA-CH-5761     TCGA-CH-5762     TCGA-CH-5763 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5764     TCGA-CH-5765     TCGA-CH-5766     TCGA-CH-5767 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5768     TCGA-CH-5769     TCGA-CH-5771     TCGA-CH-5772 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5788     TCGA-CH-5789     TCGA-CH-5790     TCGA-CH-5791 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5792     TCGA-CH-5794     TCGA-EJ-5495     TCGA-EJ-5496 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5497     TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5502     TCGA-EJ-5503     TCGA-EJ-5504     TCGA-EJ-5505 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5506     TCGA-EJ-5507     TCGA-EJ-5508     TCGA-EJ-5509 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5510     TCGA-EJ-5511     TCGA-EJ-5512     TCGA-EJ-5514 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5515     TCGA-EJ-5516     TCGA-EJ-5517     TCGA-EJ-5518 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5519     TCGA-EJ-5521     TCGA-EJ-5522     TCGA-EJ-5524 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5525     TCGA-EJ-5526     TCGA-EJ-5527     TCGA-EJ-5530 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5531     TCGA-EJ-5532     TCGA-EJ-5542     TCGA-EJ-7115 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7123     TCGA-EJ-7125     TCGA-EJ-7218     TCGA-EJ-7312 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7318 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7321     TCGA-EJ-7325     TCGA-EJ-7327     TCGA-EJ-7330 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7331     TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7784     TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7797     TCGA-EJ-8468     TCGA-EJ-8469     TCGA-EJ-8472 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-8474     TCGA-EJ-A46B     TCGA-EJ-A46D     TCGA-EJ-A46E 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A46F     TCGA-EJ-A46G     TCGA-EJ-A46H     TCGA-EJ-A46I 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A65B     TCGA-EJ-A65D     TCGA-EJ-A65E     TCGA-EJ-A65F 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A65G     TCGA-EJ-A65J     TCGA-EJ-A65M     TCGA-EJ-A6RA 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A6RC     TCGA-EJ-A7NF     TCGA-EJ-A7NG     TCGA-EJ-A7NH 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A7NJ     TCGA-EJ-A7NK     TCGA-EJ-A7NM     TCGA-EJ-A7NN 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-A8FN     TCGA-EJ-A8FO     TCGA-EJ-A8FP     TCGA-EJ-A8FS 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-FC-A5OB     TCGA-FC-A66V     TCGA-FC-A6HD     TCGA-FC-A8O0 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6329     TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6338     TCGA-G9-6339     TCGA-G9-6342     TCGA-G9-6343 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6347     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6354     TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6379     TCGA-G9-6384 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6385     TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6498 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6499     TCGA-G9-7510     TCGA-G9-7519     TCGA-G9-7521 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-7522     TCGA-G9-7523     TCGA-G9-7525     TCGA-H9-7775 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-H9-A6BX     TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7209     TCGA-HC-7210 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7736     TCGA-HC-7737     TCGA-HC-7740     TCGA-HC-7744 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7747     TCGA-HC-7748     TCGA-HC-7749     TCGA-HC-7750 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7752     TCGA-HC-7817     TCGA-HC-7818     TCGA-HC-7819 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7821     TCGA-HC-8216     TCGA-HC-8257     TCGA-HC-8258 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-8259     TCGA-HC-8260     TCGA-HC-8262     TCGA-HC-8265 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-A76W     TCGA-HC-A76X     TCGA-HC-A8CY     TCGA-HC-A8D0 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-A8D1     TCGA-HI-7168     TCGA-HI-7169     TCGA-HI-7170 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HI-7171     TCGA-J4-8198     TCGA-J4-8200     TCGA-J4-A67K 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A67L     TCGA-J4-A67M     TCGA-J4-A67N     TCGA-J4-A67O 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A67Q     TCGA-J4-A67R     TCGA-J4-A67S     TCGA-J4-A67T 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A6G1     TCGA-J4-A6G3     TCGA-J4-A6M7     TCGA-J4-A83I 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A83J     TCGA-J4-A83K     TCGA-J4-A83L     TCGA-J4-A83M 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J4-A83N     TCGA-J9-A52B     TCGA-J9-A52C     TCGA-J9-A52D 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J9-A52E     TCGA-J9-A8CL     TCGA-J9-A8CM     TCGA-J9-A8CN 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-J9-A8CP     TCGA-KC-A4BL     TCGA-KC-A4BN     TCGA-KC-A4BO 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KC-A4BR     TCGA-KC-A4BV     TCGA-KC-A7F3     TCGA-KC-A7F5 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KC-A7F6     TCGA-KC-A7FA     TCGA-KC-A7FD     TCGA-KC-A7FE 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A59V     TCGA-KK-A59Y     TCGA-KK-A59Z     TCGA-KK-A5A1 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6DY     TCGA-KK-A6E0     TCGA-KK-A6E1     TCGA-KK-A6E2 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6E3     TCGA-KK-A6E4     TCGA-KK-A6E5     TCGA-KK-A6E6 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A6E7     TCGA-KK-A6E8     TCGA-KK-A7AQ     TCGA-KK-A7AU 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A7AV     TCGA-KK-A7AW     TCGA-KK-A7AY     TCGA-KK-A7B0 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A7B1     TCGA-KK-A7B2     TCGA-KK-A7B3     TCGA-KK-A7B4 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A8I4     TCGA-KK-A8I5     TCGA-KK-A8I7     TCGA-KK-A8I8 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A8I9     TCGA-KK-A8IA     TCGA-KK-A8IC     TCGA-KK-A8ID 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A8IF     TCGA-KK-A8IG     TCGA-KK-A8IH     TCGA-KK-A8II 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-KK-A8IJ     TCGA-KK-A8IK     TCGA-KK-A8IL     TCGA-KK-A8IM 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-M7-A723     TCGA-QU-A6IL     TCGA-QU-A6IM     TCGA-QU-A6IN 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-QU-A6IO     TCGA-QU-A6IP     TCGA-SU-A7E7     TCGA-V1-A8MF 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-V1-A8MG     TCGA-V1-A8MJ     TCGA-V1-A8MK     TCGA-V1-A8ML 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-V1-A8MM     TCGA-V1-A8MU     TCGA-V1-A8WL     TCGA-V1-A8WN 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-V1-A8WS     TCGA-V1-A8WV     TCGA-V1-A8X3     TCGA-VN-A88I 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VN-A88K     TCGA-VN-A88L     TCGA-VN-A88N     TCGA-VN-A88O 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VN-A88P     TCGA-VN-A88Q     TCGA-VN-A88R     TCGA-VP-A872 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A875     TCGA-VP-A876     TCGA-VP-A878     TCGA-VP-A879 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A87B     TCGA-VP-A87C     TCGA-VP-A87D     TCGA-VP-A87E 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-VP-A87H     TCGA-VP-A87J     TCGA-VP-A87K     TCGA-WW-A8ZI 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-X4-A8KQ     TCGA-XA-A8JR     TCGA-XJ-A83F     TCGA-XJ-A83G 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-XJ-A83H     TCGA-XJ-A9DI     TCGA-XJ-A9DK     TCGA-XJ-A9DX 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-Y6-A8TL     TCGA-YJ-A8SW     TCGA-YL-A8HJ     TCGA-YL-A8HK 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8HL     TCGA-YL-A8HM     TCGA-YL-A8HO     TCGA-YL-A8S8 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8S9     TCGA-YL-A8SA     TCGA-YL-A8SB     TCGA-YL-A8SC 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8SF     TCGA-YL-A8SH     TCGA-YL-A8SJ     TCGA-YL-A8SK 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8SL     TCGA-YL-A8SO     TCGA-YL-A8SP     TCGA-YL-A8SQ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A8SR     TCGA-YL-A9WH     TCGA-YL-A9WI     TCGA-YL-A9WJ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-YL-A9WK     TCGA-ZG-A8QZ 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACPT MUTATED       0                         0     1
  ACPT WILD-TYPE     2                         7   146
D52V14, multiclass
[1] "Remove cluster labels:" "ACPT MUTATED"          
clus
  ACPT MUTATED ACPT WILD-TYPE 
             1            155 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7330     TCGA-EJ-7331     TCGA-EJ-7781 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784     TCGA-EJ-7785 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789     TCGA-EJ-7791 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794     TCGA-EJ-7797 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329     TCGA-G9-6332 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338     TCGA-G9-6342 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351     TCGA-G9-6353 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362     TCGA-G9-6363 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366     TCGA-G9-6367 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371     TCGA-G9-6373 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384     TCGA-G9-6385 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499     TCGA-H9-7775 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078     TCGA-HC-7079 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209     TCGA-HC-7210 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213     TCGA-HC-7230 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7231     TCGA-HC-7232     TCGA-HC-7233     TCGA-HC-7736 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171 
"ACPT WILD-TYPE" "ACPT WILD-TYPE" "ACPT WILD-TYPE" 

Clustering(53) Variable = AP4B1 MUTATION ANALYSIS
D53V1, survival
                 sevent
clus2               0   1
  AP4B1 MUTATED     5   0
  AP4B1 WILD-TYPE 407   7
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              5             414 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              0               7 
$`AP4B1 MUTATED`
TCGA-CH-5740 TCGA-CH-5768 TCGA-KK-A8IG TCGA-VP-A87B TCGA-Y6-A8TL 
        1.02        24.03        82.36        85.18        25.48 

$`AP4B1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 
       25.35         2.99         6.97        22.06        12.99        13.97 
TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 
        1.97         2.99        24.03         1.02        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 TCGA-CH-5771 
        1.02        23.01         1.02        15.06         2.04        13.02 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.98        26.99         9.99        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       29.00        27.16        33.11        19.56        13.32        29.79 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       46.52        44.88        26.30        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IH 
       63.48         2.73        67.43        69.27        26.43        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
      109.58        97.41        23.93        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
        2.99        31.99         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  AP4B1 MUTATED AP4B1 WILD-TYPE 
           1.02            0.72 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
          85.18          165.17 
  AP4B1 MUTATED AP4B1 WILD-TYPE 
          25.48           27.34 
[1] "1.0 - 85.2 (25.5)"  "0.7 - 165.2 (27.3)"
[1] "hr="     "9200000"
D53V2, continuous
                 vv
clus               T2  T3  T4
  AP4B1 MUTATED     2   3   0
  AP4B1 WILD-TYPE 170 236   6
D53V3, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  T2             2             170
  T3             3             236
  T4             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"
D53V4, binary
                 cls
clus                0   1
  AP4B1 MUTATED     5   0
  AP4B1 WILD-TYPE 294  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      5    0
  AP4B1 WILD-TYPE  294   58
   clus
vv  AP4B1 MUTATED AP4B1 WILD-TYPE
  0             5             294
  1             0              58
[1] 2 2
[1] FALSE
D53V5, binary
                 cls
clus                0   1
  AP4B1 MUTATED     0   5
  AP4B1 WILD-TYPE  15 400
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AP4B1 MUTATED      0    5
  AP4B1 WILD-TYPE   15  400
                                        clus
vv                                       AP4B1 MUTATED AP4B1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                5             400
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  AP4B1 MUTATED     4   1   0   0
  AP4B1 WILD-TYPE 279 102   5  15
D53V6, multiclass
    clus
vv   AP4B1 MUTATED AP4B1 WILD-TYPE
  R0             4             279
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, continuous
D53V8, continuous
D53V9, continuous
D53V10, continuous
D53V11, continuous
D53V12, continuous
D53V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AP4B1 MUTATED       0                         0     2
  AP4B1 WILD-TYPE     2                         7   145
D53V14, multiclass
[1] "Remove cluster labels:" "AP4B1 MUTATED"         
clus
  AP4B1 MUTATED AP4B1 WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5741 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745      TCGA-CH-5746 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751      TCGA-CH-5752 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761      TCGA-CH-5762 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765      TCGA-CH-5766 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5767      TCGA-CH-5769      TCGA-CH-5771      TCGA-CH-5772 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5788      TCGA-CH-5789      TCGA-CH-5790      TCGA-CH-5791 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-CH-5792      TCGA-CH-5794      TCGA-EJ-5494      TCGA-EJ-5495 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5496      TCGA-EJ-5497      TCGA-EJ-5498      TCGA-EJ-5499 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5501      TCGA-EJ-5503      TCGA-EJ-5504      TCGA-EJ-5505 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5506      TCGA-EJ-5507      TCGA-EJ-5508      TCGA-EJ-5509 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5510      TCGA-EJ-5511      TCGA-EJ-5512      TCGA-EJ-5514 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5515      TCGA-EJ-5516      TCGA-EJ-5517      TCGA-EJ-5518 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5519      TCGA-EJ-5521      TCGA-EJ-5522      TCGA-EJ-5524 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5525      TCGA-EJ-5526      TCGA-EJ-5527      TCGA-EJ-5530 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542      TCGA-EJ-7115 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314      TCGA-EJ-7315 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327      TCGA-EJ-7328 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781      TCGA-EJ-7782 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785      TCGA-EJ-7786 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791      TCGA-EJ-7792 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797      TCGA-FC-7708 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332      TCGA-G9-6333 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342      TCGA-G9-6343 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353      TCGA-G9-6356 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363      TCGA-G9-6364 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367      TCGA-G9-6369 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373      TCGA-G9-6377 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385      TCGA-G9-6494 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775      TCGA-HC-7075 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7077      TCGA-HC-7078      TCGA-HC-7079      TCGA-HC-7080 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"AP4B1 WILD-TYPE" "AP4B1 WILD-TYPE" 

Clustering(54) Variable = RAG1 MUTATION ANALYSIS
D54V1, survival
                sevent
clus2              0   1
  RAG1 MUTATED     9   0
  RAG1 WILD-TYPE 403   7
  RAG1 MUTATED RAG1 WILD-TYPE 
             9            410 
  RAG1 MUTATED RAG1 WILD-TYPE 
             0              7 
$`RAG1 MUTATED`
TCGA-CH-5768 TCGA-EJ-5502 TCGA-HC-7230 TCGA-HC-7742 TCGA-HC-7820 TCGA-HC-A8D1 
       24.03        26.30         1.68         1.48        24.56        18.84 
TCGA-J4-8198 TCGA-KK-A8I6 TCGA-YL-A8S8 
       20.19        21.96        62.14 

$`RAG1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5769 
       12.00         1.02        23.01         1.02        15.06         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       29.79        46.52        44.88        45.73        28.93        30.31 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       27.19        23.90        38.93        48.13        36.69        48.53 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       38.53        36.23        60.23        46.55        47.80        52.27 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
       64.50        51.88        68.35        43.07        36.66        38.76 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       39.75        60.23        41.85        47.87        29.06        88.34 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 TCGA-EJ-7315 
       74.10        93.70        83.57        36.13        37.81        33.14 
TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 TCGA-EJ-7328 
       25.35        33.83        27.09        35.18        30.35        27.68 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28        24.39        23.90        38.37        25.87        25.68 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 
       20.55        14.53        14.14        18.15        19.59        17.29 
TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 TCGA-EJ-8470 
        3.75        23.05        19.92        77.16        76.41        38.10 
TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E TCGA-EJ-A46F 
       24.85        25.18        21.60        20.58        17.23        25.74 
TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D TCGA-EJ-A65E 
       21.96        23.80        21.96        23.34        12.92        13.71 
TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       18.41        21.90        14.83         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        2.37        38.17        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 
       23.57         1.68        23.70        24.59        26.04         1.97 
TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7821 
       17.16        25.71        30.51        30.84        17.85        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HI-7168 TCGA-HI-7169 
        7.00         4.93         9.53        25.48        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       82.92        43.69        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       23.67        14.37        20.28        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        86.40        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       20.94        67.99       101.79        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS 
       14.73        39.29        53.16        52.08        30.38        15.58 
TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M 
       22.55         6.64         8.84        25.51        24.53         6.21 
TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 
       15.52        15.81        41.42        44.91        25.78       111.39 
TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C 
       75.91       109.58        97.41        23.93        85.18        55.56 
TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI 
       60.92        66.97        21.80        53.36        42.94        14.76 
TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H 
       45.47        32.19         3.91        37.05        38.04        42.08 
TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW 
       48.03         9.04         2.99        31.99        25.48         4.87 
TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 
       52.96        49.02        51.45        48.72        71.77        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  RAG1 MUTATED RAG1 WILD-TYPE 
          1.48           0.72 
  RAG1 MUTATED RAG1 WILD-TYPE 
         62.14         165.17 
  RAG1 MUTATED RAG1 WILD-TYPE 
        21.960         27.795 
[1] "1.5 - 62.1 (22.0)"  "0.7 - 165.2 (27.8)"
[1] "hr="     "9100000"
D54V2, continuous
                vv
clus              T2  T3  T4
  RAG1 MUTATED     4   5   0
  RAG1 WILD-TYPE 168 234   6
D54V3, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  T2            4            168
  T3            5            234
  T4            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"
D54V4, binary
                cls
clus               0   1
  RAG1 MUTATED     7   0
  RAG1 WILD-TYPE 292  58
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      7    0
  RAG1 WILD-TYPE  292   58
   clus
vv  RAG1 MUTATED RAG1 WILD-TYPE
  0            7            292
  1            0             58
[1] 2 2
[1] FALSE
D54V5, binary
                cls
clus               0   1
  RAG1 MUTATED     0   9
  RAG1 WILD-TYPE  15 396
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAG1 MUTATED      0    9
  RAG1 WILD-TYPE   15  396
                                        clus
vv                                       RAG1 MUTATED RAG1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               9            396
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  RAG1 MUTATED     7   1   0   0
  RAG1 WILD-TYPE 276 102   5  15
D54V6, multiclass
    clus
vv   RAG1 MUTATED RAG1 WILD-TYPE
  R0            7            276
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, continuous
D54V8, continuous
D54V9, continuous
D54V10, continuous
D54V11, continuous
D54V12, continuous
D54V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAG1 MUTATED       0                         0     4
  RAG1 WILD-TYPE     2                         7   143
D54V14, multiclass
                           clus
vv                          RAG1 MUTATED RAG1 WILD-TYPE
  ASIAN                                0              2
  BLACK OR AFRICAN AMERICAN            0              7
  WHITE                                4            143
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = APC MUTATION ANALYSIS
D55V1, survival
               sevent
clus2             0   1
  APC MUTATED     8   0
  APC WILD-TYPE 404   7
  APC MUTATED APC WILD-TYPE 
            8           411 
  APC MUTATED APC WILD-TYPE 
            0             7 
$`APC MUTATED`
TCGA-EJ-7325 TCGA-EJ-A8FS TCGA-HC-7819 TCGA-HC-A632 TCGA-HC-A8D0 TCGA-YL-A8S8 
       35.18         8.75        17.85         2.01        25.48        62.14 
TCGA-YL-A8SO TCGA-YL-A9WI 
      114.38        53.36 

$`APC WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FU 
        4.21         6.48        10.82         9.27         9.83         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 
        2.17         2.27        22.55        17.95        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A6AL 
       15.88         1.15        22.36         0.76         1.78         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D1 TCGA-HI-7168 
        4.41         7.00         4.93         9.53        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       48.72        71.77        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SP 
       45.14        28.77        45.86        46.29        32.45        71.34 
TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW 
       62.79         8.98        14.04        60.99        62.37         3.09 
TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       14.53        13.28        10.13 

  APC MUTATED APC WILD-TYPE 
         2.01          0.72 
  APC MUTATED APC WILD-TYPE 
       114.38        165.17 
  APC MUTATED APC WILD-TYPE 
        30.33         27.29 
[1] "2.0 - 114.4 (30.3)" "0.7 - 165.2 (27.3)"
[1] "hr="     "2.8e+07"
D55V2, continuous
               vv
clus             T2  T3  T4
  APC MUTATED     2   6   0
  APC WILD-TYPE 170 233   6
D55V3, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  T2           2           170
  T3           6           233
  T4           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"
D55V4, binary
               cls
clus              0   1
  APC MUTATED     6   1
  APC WILD-TYPE 293  57
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      6    1
  APC WILD-TYPE  293   57
   clus
vv  APC MUTATED APC WILD-TYPE
  0           6           293
  1           1            57
[1] 2 2
[1] FALSE
D55V5, binary
               cls
clus              0   1
  APC MUTATED     0   8
  APC WILD-TYPE  15 397
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED      0    8
  APC WILD-TYPE   15  397
                                        clus
vv                                       APC MUTATED APC WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE           0            15
  PROSTATE ADENOCARCINOMA ACINAR TYPE              8           397
[1] 2 2
[1] FALSE
               vv
clus             R0  R1  R2  RX
  APC MUTATED     5   2   1   0
  APC WILD-TYPE 278 101   4  15
D55V6, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0           5           278
  R1           2           101
  R2           1             4
  RX           0            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, continuous
D55V8, continuous
D55V9, continuous
D55V10, continuous
D55V11, continuous
D55V12, continuous
D55V13, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  APC MUTATED       0                         0     1
  APC WILD-TYPE     2                         7   146
D55V14, multiclass
[1] "Remove cluster labels:" "APC MUTATED"           
clus
  APC MUTATED APC WILD-TYPE 
            1           155 
   TCGA-CH-5737    TCGA-CH-5738    TCGA-CH-5739    TCGA-CH-5740    TCGA-CH-5741 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5743    TCGA-CH-5744    TCGA-CH-5745    TCGA-CH-5746    TCGA-CH-5748 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5750    TCGA-CH-5751    TCGA-CH-5752    TCGA-CH-5753    TCGA-CH-5754 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5761    TCGA-CH-5762    TCGA-CH-5763    TCGA-CH-5764    TCGA-CH-5765 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5766    TCGA-CH-5767    TCGA-CH-5768    TCGA-CH-5769    TCGA-CH-5771 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5772    TCGA-CH-5788    TCGA-CH-5789    TCGA-CH-5790    TCGA-CH-5791 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-CH-5792    TCGA-CH-5794    TCGA-EJ-5494    TCGA-EJ-5495    TCGA-EJ-5496 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5497    TCGA-EJ-5498    TCGA-EJ-5499    TCGA-EJ-5501    TCGA-EJ-5503 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5504    TCGA-EJ-5505    TCGA-EJ-5506    TCGA-EJ-5507    TCGA-EJ-5508 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5509    TCGA-EJ-5510    TCGA-EJ-5511    TCGA-EJ-5512    TCGA-EJ-5514 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5515    TCGA-EJ-5516    TCGA-EJ-5517    TCGA-EJ-5518    TCGA-EJ-5519 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5521    TCGA-EJ-5522    TCGA-EJ-5524    TCGA-EJ-5525    TCGA-EJ-5526 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-5527    TCGA-EJ-5530    TCGA-EJ-5531    TCGA-EJ-5532    TCGA-EJ-5542 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7115    TCGA-EJ-7123    TCGA-EJ-7125    TCGA-EJ-7314    TCGA-EJ-7315 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7317    TCGA-EJ-7321    TCGA-EJ-7327    TCGA-EJ-7328    TCGA-EJ-7330 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7331    TCGA-EJ-7781    TCGA-EJ-7782    TCGA-EJ-7783    TCGA-EJ-7784 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7785    TCGA-EJ-7786    TCGA-EJ-7788    TCGA-EJ-7789    TCGA-EJ-7791 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-EJ-7792    TCGA-EJ-7793    TCGA-EJ-7794    TCGA-EJ-7797    TCGA-FC-7708 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-FC-7961    TCGA-G9-6329    TCGA-G9-6332    TCGA-G9-6333    TCGA-G9-6336 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6338    TCGA-G9-6342    TCGA-G9-6343    TCGA-G9-6348    TCGA-G9-6351 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6353    TCGA-G9-6356    TCGA-G9-6361    TCGA-G9-6362    TCGA-G9-6363 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6364    TCGA-G9-6365    TCGA-G9-6366    TCGA-G9-6367    TCGA-G9-6369 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6370    TCGA-G9-6371    TCGA-G9-6373    TCGA-G9-6377    TCGA-G9-6378 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-G9-6384    TCGA-G9-6385    TCGA-G9-6494    TCGA-G9-6496    TCGA-G9-6499 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-H9-7775    TCGA-HC-7075    TCGA-HC-7077    TCGA-HC-7078    TCGA-HC-7079 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7080    TCGA-HC-7081    TCGA-HC-7209    TCGA-HC-7210    TCGA-HC-7211 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7212    TCGA-HC-7213    TCGA-HC-7230    TCGA-HC-7231    TCGA-HC-7232 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7233    TCGA-HC-7736    TCGA-HC-7737    TCGA-HC-7738    TCGA-HC-7740 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7742    TCGA-HC-7744    TCGA-HC-7745    TCGA-HC-7747    TCGA-HC-7748 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7749    TCGA-HC-7750    TCGA-HC-7752    TCGA-HC-7818    TCGA-HC-7820 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-HC-7821    TCGA-HI-7168    TCGA-HI-7169    TCGA-HI-7170    TCGA-HI-7171 
"APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" "APC WILD-TYPE" 

Clustering(56) Variable = MSLNL MUTATION ANALYSIS
D56V1, survival
                 sevent
clus2               0   1
  MSLNL MUTATED     3   1
  MSLNL WILD-TYPE 409   6
  MSLNL MUTATED MSLNL WILD-TYPE 
              4             415 
  MSLNL MUTATED MSLNL WILD-TYPE 
              1               6 
$`MSLNL MUTATED`
TCGA-EJ-5530 TCGA-HC-7078 TCGA-HC-8261 TCGA-YL-A9WJ 
       60.23        65.26        17.95        60.99 

$`MSLNL WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       36.66        38.76        39.75        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7079 TCGA-HC-7080 
        6.08        30.94         3.68        19.76         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8262 TCGA-HC-8264 
       23.87         2.17         2.27        22.55        22.32         1.58 
TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 
       15.88         1.15        22.36         0.76         1.78         2.01 
TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS 
        2.20         1.61        17.42         2.33         3.48         1.45 
TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 
        1.25         4.41         7.00         4.93         9.53        25.48 
TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 
       18.84        78.61        88.24        82.92        43.69        20.19 
TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O 
       12.30        33.01        25.32        30.94        16.54        27.58 
TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 
       32.05        29.92        27.39         6.02        25.28        27.91 
TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M 
       16.83        22.52        22.88        10.78        23.67        14.37 
TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL 
       20.28        13.87         5.85         6.97        10.62        13.32 
TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO 
       15.22        40.67        12.69        30.71        59.67        19.96 
TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       44.35        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z 
        8.88        11.57       113.10        56.28        44.68        86.40 
TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 
       77.72       115.86        30.02        54.54       165.17        67.59 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       14.04        53.36        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  MSLNL MUTATED MSLNL WILD-TYPE 
          17.95            0.72 
  MSLNL MUTATED MSLNL WILD-TYPE 
          65.26          165.17 
  MSLNL MUTATED MSLNL WILD-TYPE 
          60.61           27.19 
[1] "17.9 - 65.3 (60.6)" "0.7 - 165.2 (27.2)"
[1] "hr=" "13" 
D56V2, continuous
                 vv
clus               T2  T3  T4
  MSLNL MUTATED     2   2   0
  MSLNL WILD-TYPE 170 237   6
D56V3, multiclass
    clus
vv   MSLNL MUTATED MSLNL WILD-TYPE
  T2             2             170
  T3             2             237
  T4             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"
D56V4, binary
                 cls
clus                0   1
  MSLNL MUTATED     2   1
  MSLNL WILD-TYPE 297  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSLNL MUTATED      2    1
  MSLNL WILD-TYPE  297   57
   clus
vv  MSLNL MUTATED MSLNL WILD-TYPE
  0             2             297
  1             1              57
[1] 2 2
[1] FALSE
D56V5, binary
                 cls
clus                0   1
  MSLNL MUTATED     0   4
  MSLNL WILD-TYPE  15 401
[1] "tbl2"
                 cls
clus              [,1] [,2]
  MSLNL MUTATED      0    4
  MSLNL WILD-TYPE   15  401
                                        clus
vv                                       MSLNL MUTATED MSLNL WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                4             401
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  MSLNL MUTATED     3   1   0   0
  MSLNL WILD-TYPE 280 102   5  15
D56V6, multiclass
    clus
vv   MSLNL MUTATED MSLNL WILD-TYPE
  R0             3             280
  R1             1             102
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, continuous
D56V8, continuous
D56V9, continuous
D56V10, continuous
D56V11, continuous
D56V12, continuous
D56V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MSLNL MUTATED       0                         0     2
  MSLNL WILD-TYPE     2                         7   145
D56V14, multiclass
[1] "Remove cluster labels:" "MSLNL MUTATED"         
clus
  MSLNL MUTATED MSLNL WILD-TYPE 
              2             154 
     TCGA-CH-5737      TCGA-CH-5738      TCGA-CH-5739      TCGA-CH-5740 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5741      TCGA-CH-5743      TCGA-CH-5744      TCGA-CH-5745 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5746      TCGA-CH-5748      TCGA-CH-5750      TCGA-CH-5751 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5752      TCGA-CH-5753      TCGA-CH-5754      TCGA-CH-5761 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5762      TCGA-CH-5763      TCGA-CH-5764      TCGA-CH-5765 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5766      TCGA-CH-5767      TCGA-CH-5768      TCGA-CH-5769 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5771      TCGA-CH-5772      TCGA-CH-5788      TCGA-CH-5789 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-CH-5790      TCGA-CH-5791      TCGA-CH-5792      TCGA-CH-5794 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5494      TCGA-EJ-5495      TCGA-EJ-5496      TCGA-EJ-5497 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5498      TCGA-EJ-5499      TCGA-EJ-5501      TCGA-EJ-5503 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5504      TCGA-EJ-5505      TCGA-EJ-5506      TCGA-EJ-5507 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5508      TCGA-EJ-5509      TCGA-EJ-5510      TCGA-EJ-5511 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5512      TCGA-EJ-5514      TCGA-EJ-5515      TCGA-EJ-5516 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5517      TCGA-EJ-5518      TCGA-EJ-5519      TCGA-EJ-5521 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5522      TCGA-EJ-5524      TCGA-EJ-5525      TCGA-EJ-5526 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-5527      TCGA-EJ-5531      TCGA-EJ-5532      TCGA-EJ-5542 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7115      TCGA-EJ-7123      TCGA-EJ-7125      TCGA-EJ-7314 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7315      TCGA-EJ-7317      TCGA-EJ-7321      TCGA-EJ-7327 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7328      TCGA-EJ-7330      TCGA-EJ-7331      TCGA-EJ-7781 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7782      TCGA-EJ-7783      TCGA-EJ-7784      TCGA-EJ-7785 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7786      TCGA-EJ-7788      TCGA-EJ-7789      TCGA-EJ-7791 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-EJ-7792      TCGA-EJ-7793      TCGA-EJ-7794      TCGA-EJ-7797 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-FC-7708      TCGA-FC-7961      TCGA-G9-6329      TCGA-G9-6332 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6333      TCGA-G9-6336      TCGA-G9-6338      TCGA-G9-6342 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6343      TCGA-G9-6348      TCGA-G9-6351      TCGA-G9-6353 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6356      TCGA-G9-6361      TCGA-G9-6362      TCGA-G9-6363 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6364      TCGA-G9-6365      TCGA-G9-6366      TCGA-G9-6367 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6369      TCGA-G9-6370      TCGA-G9-6371      TCGA-G9-6373 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6377      TCGA-G9-6378      TCGA-G9-6384      TCGA-G9-6385 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-G9-6494      TCGA-G9-6496      TCGA-G9-6499      TCGA-H9-7775 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7075      TCGA-HC-7077      TCGA-HC-7079      TCGA-HC-7080 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7081      TCGA-HC-7209      TCGA-HC-7210      TCGA-HC-7211 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7212      TCGA-HC-7213      TCGA-HC-7230      TCGA-HC-7231 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7232      TCGA-HC-7233      TCGA-HC-7736      TCGA-HC-7737 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7738      TCGA-HC-7740      TCGA-HC-7742      TCGA-HC-7744 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7745      TCGA-HC-7747      TCGA-HC-7748      TCGA-HC-7749 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7750      TCGA-HC-7752      TCGA-HC-7818      TCGA-HC-7819 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HC-7820      TCGA-HC-7821      TCGA-HI-7168      TCGA-HI-7169 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 
     TCGA-HI-7170      TCGA-HI-7171 
"MSLNL WILD-TYPE" "MSLNL WILD-TYPE" 

Clustering(57) Variable = GAB2 MUTATION ANALYSIS
D57V1, survival
                sevent
clus2              0   1
  GAB2 MUTATED     5   0
  GAB2 WILD-TYPE 407   7
  GAB2 MUTATED GAB2 WILD-TYPE 
             5            414 
  GAB2 MUTATED GAB2 WILD-TYPE 
             0              7 
$`GAB2 MUTATED`
TCGA-EJ-A46F TCGA-EJ-A65J TCGA-HC-7232 TCGA-HC-8264 TCGA-J4-A67T 
       25.74        14.83        38.17         1.58         6.02 

$`GAB2 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       17.23        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65M TCGA-EJ-A6RA TCGA-EJ-A6RC 
       13.71        18.41        21.90         7.56        11.61        28.70 
TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK TCGA-EJ-A7NM 
        8.22        14.20        15.58         6.48        15.65         4.21 
TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS TCGA-EJ-A8FU 
        6.48        10.82         9.27         9.83         8.75         4.54 
TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD 
       28.41        15.42        13.45        22.36        17.23        16.24 
TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.78        41.62        87.35        81.04        67.99        66.67 
TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 
       83.87        55.76        18.21        68.68        49.81        46.16 
TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       50.70        49.35        47.15        46.52        47.44        45.30 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       39.39        44.81         3.32        40.18        39.95        38.01 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 TCGA-G9-6384 
       40.31        26.66        31.50        37.97        58.45        25.15 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 
       27.29        58.22        56.75        64.18        50.73        38.96 
TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 
       27.91        30.97        35.34        28.18        32.68         6.08 
TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 
       30.94         3.68        19.76        65.26         2.93        36.36 
TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 
       37.35        14.47        28.54         0.79        28.60        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 
        1.68         2.37        44.55         0.72         2.10        31.69 
TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 
       23.57         1.48         1.68        23.70        24.59        26.04 
TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 
        1.97        17.16        25.71        30.51        30.84        17.85 
TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 
       24.56        31.43        19.36        22.42        28.27        23.87 
TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8265 
        2.17         2.27        22.55        17.95        22.32        15.88 
TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL 
        1.15        22.36         0.76         1.78         2.01         2.20 
TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX 
        1.61        17.42         2.33         3.48         1.45         1.25 
TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 
        4.41         7.00         4.93         9.53        25.48        18.84 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 
       78.61        88.24        82.92        43.69        20.19        12.30 
TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q 
       33.01        25.32        30.94        16.54        27.58        32.05 
TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       29.92        27.39        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY 
      113.10        56.28        44.68        86.40        77.72       115.86 
TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 
       30.02        54.54       165.17        67.59       115.13        49.25 
TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU 
      113.33        67.07        58.19         6.44        52.93        58.36 
TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 
       27.02        34.65        51.68        49.94        32.84        34.95 
TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 
       36.13        29.56        20.94        67.99       101.79        21.96 
TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC 
       65.82        31.79        32.91        63.48         2.73        67.43 
TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ 
       69.27        26.43        82.36        66.18       113.98        51.25 
TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 
       51.39        20.65        47.28         5.19        21.14        12.62 
TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL 
       13.15        34.85        25.08        29.23        18.84         3.19 
TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF 
       41.00       140.19       122.17        86.14        18.12        41.23 
TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU 
       28.18        40.44        16.70        14.73        39.29        53.16 
TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I 
       52.08        30.38        15.58        22.55         6.64         8.84 
TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P 
       25.51        24.53         6.21        15.52        15.81        41.42 
TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 
       44.91        25.78       111.39        75.91       109.58        97.41 
TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H 
       23.93        85.18        55.56        60.92        66.97        21.80 
TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       53.36        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  GAB2 MUTATED GAB2 WILD-TYPE 
          1.58           0.72 
  GAB2 MUTATED GAB2 WILD-TYPE 
         38.17         165.17 
  GAB2 MUTATED GAB2 WILD-TYPE 
        14.830         27.485 
[1] "1.6 - 38.2 (14.8)"  "0.7 - 165.2 (27.5)"
[1] "hr="     "3300000"
D57V2, continuous
                vv
clus              T2  T3  T4
  GAB2 MUTATED     1   4   0
  GAB2 WILD-TYPE 171 235   6
D57V3, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  T2            1            171
  T3            4            235
  T4            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"
D57V4, binary
                cls
clus               0   1
  GAB2 MUTATED     1   2
  GAB2 WILD-TYPE 298  56
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      1    2
  GAB2 WILD-TYPE  298   56
   clus
vv  GAB2 MUTATED GAB2 WILD-TYPE
  0            1            298
  1            2             56
[1] 2 2
[1] FALSE
D57V5, binary
                cls
clus               0   1
  GAB2 MUTATED     0   5
  GAB2 WILD-TYPE  15 400
[1] "tbl2"
                cls
clus             [,1] [,2]
  GAB2 MUTATED      0    5
  GAB2 WILD-TYPE   15  400
                                        clus
vv                                       GAB2 MUTATED GAB2 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE            0             15
  PROSTATE ADENOCARCINOMA ACINAR TYPE               5            400
[1] 2 2
[1] FALSE
                vv
clus              R0  R1  R2  RX
  GAB2 MUTATED     4   1   0   0
  GAB2 WILD-TYPE 279 102   5  15
D57V6, multiclass
    clus
vv   GAB2 MUTATED GAB2 WILD-TYPE
  R0            4            279
  R1            1            102
  R2            0              5
  RX            0             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, continuous
D57V8, continuous
D57V9, continuous
D57V10, continuous
D57V11, continuous
D57V12, continuous
D57V13, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GAB2 MUTATED       0                         0     1
  GAB2 WILD-TYPE     2                         7   146
D57V14, multiclass
[1] "Remove cluster labels:" "GAB2 MUTATED"          
clus
  GAB2 MUTATED GAB2 WILD-TYPE 
             1            155 
    TCGA-CH-5737     TCGA-CH-5738     TCGA-CH-5739     TCGA-CH-5740 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5741     TCGA-CH-5743     TCGA-CH-5744     TCGA-CH-5745 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5746     TCGA-CH-5748     TCGA-CH-5750     TCGA-CH-5751 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5752     TCGA-CH-5753     TCGA-CH-5754     TCGA-CH-5761 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5762     TCGA-CH-5763     TCGA-CH-5764     TCGA-CH-5765 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5766     TCGA-CH-5767     TCGA-CH-5768     TCGA-CH-5769 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5771     TCGA-CH-5772     TCGA-CH-5788     TCGA-CH-5789 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-CH-5790     TCGA-CH-5791     TCGA-CH-5792     TCGA-CH-5794 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5494     TCGA-EJ-5495     TCGA-EJ-5496     TCGA-EJ-5497 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5498     TCGA-EJ-5499     TCGA-EJ-5501     TCGA-EJ-5503 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5504     TCGA-EJ-5505     TCGA-EJ-5506     TCGA-EJ-5507 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5508     TCGA-EJ-5509     TCGA-EJ-5510     TCGA-EJ-5511 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5512     TCGA-EJ-5514     TCGA-EJ-5515     TCGA-EJ-5516 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5517     TCGA-EJ-5518     TCGA-EJ-5519     TCGA-EJ-5521 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5522     TCGA-EJ-5524     TCGA-EJ-5525     TCGA-EJ-5526 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5527     TCGA-EJ-5530     TCGA-EJ-5531     TCGA-EJ-5532 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-5542     TCGA-EJ-7115     TCGA-EJ-7123     TCGA-EJ-7125 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7314     TCGA-EJ-7315     TCGA-EJ-7317     TCGA-EJ-7321 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7327     TCGA-EJ-7328     TCGA-EJ-7330     TCGA-EJ-7331 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7781     TCGA-EJ-7782     TCGA-EJ-7783     TCGA-EJ-7784 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7785     TCGA-EJ-7786     TCGA-EJ-7788     TCGA-EJ-7789 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7791     TCGA-EJ-7792     TCGA-EJ-7793     TCGA-EJ-7794 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-EJ-7797     TCGA-FC-7708     TCGA-FC-7961     TCGA-G9-6329 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6332     TCGA-G9-6333     TCGA-G9-6336     TCGA-G9-6338 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6342     TCGA-G9-6343     TCGA-G9-6348     TCGA-G9-6351 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6353     TCGA-G9-6356     TCGA-G9-6361     TCGA-G9-6362 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6363     TCGA-G9-6364     TCGA-G9-6365     TCGA-G9-6366 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6367     TCGA-G9-6369     TCGA-G9-6370     TCGA-G9-6371 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6373     TCGA-G9-6377     TCGA-G9-6378     TCGA-G9-6384 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-G9-6385     TCGA-G9-6494     TCGA-G9-6496     TCGA-G9-6499 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-H9-7775     TCGA-HC-7075     TCGA-HC-7077     TCGA-HC-7078 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7079     TCGA-HC-7080     TCGA-HC-7081     TCGA-HC-7209 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7210     TCGA-HC-7211     TCGA-HC-7212     TCGA-HC-7213 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7230     TCGA-HC-7231     TCGA-HC-7233     TCGA-HC-7736 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7737     TCGA-HC-7738     TCGA-HC-7740     TCGA-HC-7742 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7744     TCGA-HC-7745     TCGA-HC-7747     TCGA-HC-7748 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7749     TCGA-HC-7750     TCGA-HC-7752     TCGA-HC-7818 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HC-7819     TCGA-HC-7820     TCGA-HC-7821     TCGA-HI-7168 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 
    TCGA-HI-7169     TCGA-HI-7170     TCGA-HI-7171 
"GAB2 WILD-TYPE" "GAB2 WILD-TYPE" "GAB2 WILD-TYPE" 

Clustering(58) Variable = DNMT3B MUTATION ANALYSIS
D58V1, survival
                  sevent
clus2                0   1
  DNMT3B MUTATED     4   0
  DNMT3B WILD-TYPE 408   7
  DNMT3B MUTATED DNMT3B WILD-TYPE 
               4              415 
  DNMT3B MUTATED DNMT3B WILD-TYPE 
               0                7 
$`DNMT3B MUTATED`
TCGA-KK-A59V TCGA-KK-A8I9 TCGA-M7-A724 TCGA-V1-A8X3 
      113.10        32.91        29.23         6.64 

$`DNMT3B WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 
       37.81        33.14        25.35        33.83        27.09        35.18 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 
       30.35        27.68         6.28        24.39        23.90        38.37 
TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 
       25.87        25.68        20.55        14.53        14.14        18.15 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 
       19.59        17.29         3.75        23.05        19.92        77.16 
TCGA-EJ-8469 TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D 
       76.41        38.10        24.85        25.18        21.60        20.58 
TCGA-EJ-A46E TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B 
       17.23        25.74        21.96        23.80        21.96        23.34 
TCGA-EJ-A65D TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M 
       12.92        13.71        18.41        21.90        14.83         7.56 
TCGA-EJ-A6RA TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ 
       11.61        28.70         8.22        14.20        15.58         6.48 
TCGA-EJ-A7NK TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP 
       15.65         4.21         6.48        10.82         9.27         9.83 
TCGA-EJ-A8FS TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB 
        8.75         4.54        28.41        15.42        13.45        22.36 
TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
       17.23        16.24         1.78        41.62        87.35        81.04 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 
       67.99        66.67        83.87        55.76        18.21        68.68 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 
       49.81        46.16        50.70        49.35        47.15        46.52 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       47.44        45.30        39.39        44.81         3.32        40.18 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       39.95        38.01        40.31        26.66        31.50        37.97 
TCGA-G9-6379 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 
       58.45        25.15        27.29        58.22        56.75        64.18 
TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 
       50.73        38.96        27.91        30.97        35.34        28.18 
TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 
       32.68         6.08        30.94         3.68        19.76        65.26 
TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 
        2.93        36.36        37.35        14.47        28.54         0.79 
TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 
       28.60        40.08         1.68         2.37        38.17        44.55 
TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 
        0.72         2.10        31.69        23.57         1.48         1.68 
TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 
       23.70        24.59        26.04         1.97        17.16        25.71 
TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 
       30.51        30.84        17.85        24.56        31.43        19.36 
TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 
       22.42        28.27        23.87         2.17         2.27        22.55 
TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F 
       17.95        22.32         1.58        15.88         1.15        22.36 
TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO 
        0.76         1.78         2.01         2.20         1.61        17.42 
TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W 
        2.33         3.48         1.45         1.25         4.41         7.00 
TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 
        4.93         9.53        25.48        18.84        78.61        88.24 
TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L 
       82.92        43.69        20.19        12.30        33.01        25.32 
TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S 
       30.94        16.54        27.58        32.05        29.92        27.39 
TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J 
        6.02        25.28        27.91        16.83        22.52        22.88 
TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C 
       10.78        23.67        14.37        20.28        13.87         5.85 
TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP 
        6.97        10.62        13.32        15.22        40.67        12.69 
TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 
       30.71        59.67        19.96        44.35        43.66        21.86 
TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X 
        2.99         8.65        19.66         8.88        11.57        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 
       44.68        86.40        77.72       115.86        30.02        54.54 
TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 
      165.17        67.59       115.13        49.25       113.33        67.07 
TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW 
       58.19         6.44        52.93        58.36        27.02        34.65 
TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 
       51.68        49.94        32.84        34.95        36.13        29.56 
TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 
       20.94        67.99       101.79        21.96        65.82        31.79 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  DNMT3B MUTATED DNMT3B WILD-TYPE 
            6.64             0.72 
  DNMT3B MUTATED DNMT3B WILD-TYPE 
          113.10           165.17 
  DNMT3B MUTATED DNMT3B WILD-TYPE 
           31.07            27.19 
[1] "6.6 - 113.1 (31.1)" "0.7 - 165.2 (27.2)"
[1] "hr="     "9100000"
D58V2, continuous
                  vv
clus                T2  T3  T4
  DNMT3B MUTATED     1   3   0
  DNMT3B WILD-TYPE 171 236   6
D58V3, multiclass
    clus
vv   DNMT3B MUTATED DNMT3B WILD-TYPE
  T2              1              171
  T3              3              236
  T4              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"
D58V4, binary
                  cls
clus                 0   1
  DNMT3B MUTATED     4   0
  DNMT3B WILD-TYPE 295  58
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3B MUTATED      4    0
  DNMT3B WILD-TYPE  295   58
   clus
vv  DNMT3B MUTATED DNMT3B WILD-TYPE
  0              4              295
  1              0               58
[1] 2 2
[1] FALSE
D58V5, binary
                  cls
clus                 0   1
  DNMT3B MUTATED     0   4
  DNMT3B WILD-TYPE  15 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  DNMT3B MUTATED      0    4
  DNMT3B WILD-TYPE   15  401
                                        clus
vv                                       DNMT3B MUTATED DNMT3B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              401
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  DNMT3B MUTATED     1   2   0   1
  DNMT3B WILD-TYPE 282 101   5  14
D58V6, multiclass
    clus
vv   DNMT3B MUTATED DNMT3B WILD-TYPE
  R0              1              282
  R1              2              101
  R2              0                5
  RX              1               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, continuous
D58V8, continuous
D58V9, continuous
D58V10, continuous
D58V11, continuous
D58V12, continuous
D58V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DNMT3B MUTATED       0                         0     0
  DNMT3B WILD-TYPE     2                         7   147
D58V14, multiclass

Clustering(59) Variable = NCKAP1L MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  NCKAP1L MUTATED     5   0
  NCKAP1L WILD-TYPE 407   7
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                5               414 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                0                 7 
$`NCKAP1L MUTATED`
TCGA-CH-5788 TCGA-KK-A6DY TCGA-V1-A8ML TCGA-VN-A88L TCGA-VP-A87J 
       26.99       115.86        14.73        24.53        53.36 

$`NCKAP1L WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
        2.04        13.02        15.98         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 
       40.08         1.68         2.37        38.17        44.55         0.72 
TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 
        2.10        31.69        23.57         1.48         1.68        23.70 
TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 
       24.59        26.04         1.97        17.16        25.71        30.51 
TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 
       30.84        17.85        24.56        31.43        19.36        22.42 
TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 
       28.27        23.87         2.17         2.27        22.55        17.95 
TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV 
       22.32         1.58        15.88         1.15        22.36         0.76 
TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP 
        1.78         2.01         2.20         1.61        17.42         2.33 
TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X 
        3.48         1.45         1.25         4.41         7.00         4.93 
TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        9.53        25.48        18.84        78.61        88.24        82.92 
TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M 
       43.69        20.19        12.30        33.01        25.32        30.94 
TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T 
       16.54        27.58        32.05        29.92        27.39         6.02 
TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K 
       25.28        27.91        16.83        22.52        22.88        10.78 
TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D 
       23.67        14.37        20.28        13.87         5.85         6.97 
TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL 
       10.62        13.32        15.22        40.67        12.69        30.71 
TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 
       59.67        19.96        44.35        43.66        21.86         2.99 
TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X 
        8.65        19.66         8.88        11.57       113.10        56.28 
TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       44.68        86.40        77.72        30.02        54.54       165.17 
TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 
       67.59       115.13        49.25       113.33        67.07        58.19 
TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY 
        6.44        52.93        58.36        27.02        34.65        51.68 
TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 
       49.94        32.84        34.95        36.13        29.56        20.94 
TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 
       67.99       101.79        21.96        65.82        31.79        32.91 
TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG 
       63.48         2.73        67.43        69.27        26.43        82.36 
TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM 
       66.18       113.98        51.25        51.39        20.65        47.28 
TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 
        5.19        21.14        12.62        13.15        34.85        25.08 
TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO 
       29.23        18.84         3.19        41.00       140.19       122.17 
TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK 
       86.14        18.12        41.23        28.18        40.44        16.70 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        6.64         8.84        25.51         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR 
       21.80        42.94        14.76        45.47        32.19         3.91 
TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ 
       37.05        38.04        42.08        48.03         9.04         2.99 
TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL 
       31.99        25.48         4.87        52.96        49.02        51.45 
TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB 
       48.72        71.77        62.14        60.56        16.83        56.52 
TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL 
       41.46        45.14        28.77        45.86        46.29        32.45 
TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI 
      114.38        71.34        62.79         8.98        14.04        53.36 
TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       60.99        62.37         3.09        14.53        13.28        10.13 

  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
            14.73              0.72 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
           115.86            165.17 
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
            26.99             27.34 
[1] "14.7 - 115.9 (27.0)" "0.7 - 165.2 (27.3)" 
[1] "hr="     "3.1e+07"
D59V2, continuous
                   vv
clus                 T2  T3  T4
  NCKAP1L MUTATED     3   2   0
  NCKAP1L WILD-TYPE 169 237   6
D59V3, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  T2               3               169
  T3               2               237
  T4               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"
D59V4, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     3   2
  NCKAP1L WILD-TYPE 296  56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      3    2
  NCKAP1L WILD-TYPE  296   56
   clus
vv  NCKAP1L MUTATED NCKAP1L WILD-TYPE
  0               3               296
  1               2                56
[1] 2 2
[1] FALSE
D59V5, binary
                   cls
clus                  0   1
  NCKAP1L MUTATED     0   5
  NCKAP1L WILD-TYPE  15 400
[1] "tbl2"
                   cls
clus                [,1] [,2]
  NCKAP1L MUTATED      0    5
  NCKAP1L WILD-TYPE   15  400
                                        clus
vv                                       NCKAP1L MUTATED NCKAP1L WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  5               400
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  NCKAP1L MUTATED     3   1   1   0
  NCKAP1L WILD-TYPE 280 102   4  15
D59V6, multiclass
    clus
vv   NCKAP1L MUTATED NCKAP1L WILD-TYPE
  R0               3               280
  R1               1               102
  R2               1                 4
  RX               0                15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, continuous
D59V8, continuous
D59V9, continuous
D59V10, continuous
D59V11, continuous
D59V12, continuous
D59V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NCKAP1L MUTATED       0                         0     1
  NCKAP1L WILD-TYPE     2                         7   146
D59V14, multiclass
[1] "Remove cluster labels:" "NCKAP1L MUTATED"       
clus
  NCKAP1L MUTATED NCKAP1L WILD-TYPE 
                1               155 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5789        TCGA-CH-5790 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503        TCGA-EJ-5504 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507        TCGA-EJ-5508 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511        TCGA-EJ-5512 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516        TCGA-EJ-5517 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521        TCGA-EJ-5522 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526        TCGA-EJ-5527 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532        TCGA-EJ-5542 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125        TCGA-EJ-7314 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7736 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7749        TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HC-7819        TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" "NCKAP1L WILD-TYPE" 

Clustering(60) Variable = PRTFDC1 MUTATION ANALYSIS
D60V1, survival
                   sevent
clus2                 0   1
  PRTFDC1 MUTATED     3   0
  PRTFDC1 WILD-TYPE 409   7
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                3               416 
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                0                 7 
$`PRTFDC1 MUTATED`
TCGA-EJ-7314 TCGA-HC-7736 TCGA-KK-A6E3 
       37.81         0.72        67.59 

$`PRTFDC1 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7212 
       36.36        37.35        14.47        28.54         0.79        28.60 
TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7737 
       40.08         1.68         2.37        38.17        44.55         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 
       19.96        44.35        43.66        21.86         2.99         8.65 
TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59V TCGA-KK-A59X TCGA-KK-A59Y 
       19.66         8.88        11.57       113.10        56.28        44.68 
TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 
       86.40        77.72       115.86        30.02        54.54       165.17 
TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP 
      115.13        49.25       113.33        67.07        58.19         6.44 
TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ 
       52.93        58.36        27.02        34.65        51.68        49.94 
TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 
       32.84        34.95        36.13        29.56        20.94        67.99 
TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA 
      101.79        21.96        65.82        31.79        32.91        63.48 
TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH 
        2.73        67.43        69.27        26.43        82.36        66.18 
TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y 
      113.98        51.25        51.39        20.65        47.28         5.19 
TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 
       21.14        12.62        13.15        34.85        25.08        29.23 
TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP 
       18.84         3.19        41.00       140.19       122.17        86.14 
TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML 
       18.12        41.23        28.18        40.44        16.70        14.73 
TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV 
       39.29        53.16        52.08        30.38        15.58        22.55 
TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N 
        6.64         8.84        25.51        24.53         6.21        15.52 
TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 
       15.81        41.42        44.91        25.78       111.39        75.91 
TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D 
      109.58        97.41        23.93        85.18        55.56        60.92 
TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ 
       66.97        21.80        53.36        42.94        14.76        45.47 
TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI 
       32.19         3.91        37.05        38.04        42.08        48.03 
TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ 
        9.04         2.99        31.99        25.48         4.87        52.96 
TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 
       49.02        51.45        48.72        71.77        62.14        60.56 
TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ 
       16.83        56.52        41.46        45.14        28.77        45.86 
TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR 
       46.29        32.45       114.38        71.34        62.79         8.98 
TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX 
       14.04        53.36        60.99        62.37         3.09        14.53 
TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       13.28        10.13 

  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
             0.72              0.76 
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
            67.59            165.17 
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
            37.81             27.24 
[1] "0.7 - 67.6 (37.8)"  "0.8 - 165.2 (27.2)"
[1] "hr="     "3300000"
D60V2, continuous
                   vv
clus                 T2  T3  T4
  PRTFDC1 MUTATED     2   1   0
  PRTFDC1 WILD-TYPE 170 238   6
D60V3, multiclass
    clus
vv   PRTFDC1 MUTATED PRTFDC1 WILD-TYPE
  T2               2               170
  T3               1               238
  T4               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"
D60V4, binary
                   cls
clus                  0   1
  PRTFDC1 MUTATED     3   0
  PRTFDC1 WILD-TYPE 296  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRTFDC1 MUTATED      3    0
  PRTFDC1 WILD-TYPE  296   58
   clus
vv  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE
  0               3               296
  1               0                58
[1] 2 2
[1] FALSE
D60V5, binary
                   cls
clus                  0   1
  PRTFDC1 MUTATED     0   3
  PRTFDC1 WILD-TYPE  15 402
[1] "tbl2"
                   cls
clus                [,1] [,2]
  PRTFDC1 MUTATED      0    3
  PRTFDC1 WILD-TYPE   15  402
                                        clus
vv                                       PRTFDC1 MUTATED PRTFDC1 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE               0                15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                  3               402
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  PRTFDC1 MUTATED     2   0   0   0
  PRTFDC1 WILD-TYPE 281 103   5  15
D60V6, multiclass
[1] "Remove cluster labels:" "PRTFDC1 MUTATED"       
clus
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                2               404 
       TCGA-2A-A8VL        TCGA-2A-A8VO        TCGA-2A-A8VT        TCGA-2A-A8VV 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-2A-A8VX        TCGA-2A-A8W1        TCGA-2A-A8W3        TCGA-CH-5737 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740        TCGA-CH-5741 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745        TCGA-CH-5746 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7218        TCGA-EJ-7312        TCGA-EJ-7315        TCGA-EJ-7317 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7318        TCGA-EJ-7321        TCGA-EJ-7325        TCGA-EJ-7327 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-8468        TCGA-EJ-8469        TCGA-EJ-8472        TCGA-EJ-8474 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A46B        TCGA-EJ-A46E        TCGA-EJ-A46F        TCGA-EJ-A46G 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A46H        TCGA-EJ-A46I        TCGA-EJ-A65B        TCGA-EJ-A65D 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A65E        TCGA-EJ-A65F        TCGA-EJ-A65G        TCGA-EJ-A65J 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A6RA        TCGA-EJ-A6RC        TCGA-EJ-A7NF        TCGA-EJ-A7NG 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A7NH        TCGA-EJ-A7NJ        TCGA-EJ-A7NK        TCGA-EJ-A7NM 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A7NN        TCGA-EJ-A8FN        TCGA-EJ-A8FO        TCGA-EJ-A8FP 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-A8FS        TCGA-EJ-A8FU        TCGA-FC-7708        TCGA-FC-A4JI 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-FC-A5OB        TCGA-FC-A66V        TCGA-FC-A6HD        TCGA-FC-A8O0 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6329        TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6338        TCGA-G9-6339        TCGA-G9-6342        TCGA-G9-6343 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6347        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6354        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6379 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6384        TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6498        TCGA-G9-6499        TCGA-G9-7510        TCGA-G9-7519 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-7521        TCGA-G9-7522        TCGA-G9-7523        TCGA-G9-7525 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-H9-A6BX        TCGA-H9-A6BY        TCGA-HC-7075        TCGA-HC-7077 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7078        TCGA-HC-7079        TCGA-HC-7080        TCGA-HC-7081 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7209        TCGA-HC-7210        TCGA-HC-7211        TCGA-HC-7213 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7230        TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7737        TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7744        TCGA-HC-7745        TCGA-HC-7748        TCGA-HC-7749 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-8213        TCGA-HC-8216        TCGA-HC-8256 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-8257        TCGA-HC-8259        TCGA-HC-8260        TCGA-HC-8261 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-8262        TCGA-HC-8264        TCGA-HC-8265        TCGA-HC-8266 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-A48F        TCGA-HC-A4ZV        TCGA-HC-A631        TCGA-HC-A632 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-A6AL        TCGA-HC-A6AN        TCGA-HC-A6AO        TCGA-HC-A6AP 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-A6AQ        TCGA-HC-A6AS        TCGA-HC-A6HX        TCGA-HC-A6HY 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-A76W        TCGA-HC-A76X        TCGA-HC-A8CY        TCGA-HC-A8D0 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-A8D1        TCGA-HI-7168        TCGA-HI-7169        TCGA-HI-7170 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HI-7171        TCGA-J4-8200        TCGA-J4-A67K        TCGA-J4-A67L 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J4-A67M        TCGA-J4-A67N        TCGA-J4-A67O        TCGA-J4-A67R 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J4-A67S        TCGA-J4-A67T        TCGA-J4-A6G1        TCGA-J4-A6G3 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J4-A6M7        TCGA-J4-A83I        TCGA-J4-A83J        TCGA-J4-A83K 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J4-A83L        TCGA-J4-A83M        TCGA-J4-A83N        TCGA-J9-A52B 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J9-A52C        TCGA-J9-A52D        TCGA-J9-A52E        TCGA-J9-A8CL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-J9-A8CM        TCGA-J9-A8CN        TCGA-J9-A8CP        TCGA-KC-A4BL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KC-A4BN        TCGA-KC-A4BO        TCGA-KC-A4BR        TCGA-KC-A4BV 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KC-A7F3        TCGA-KC-A7F5        TCGA-KC-A7F6        TCGA-KC-A7FA 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KC-A7FD        TCGA-KC-A7FE        TCGA-KK-A59V        TCGA-KK-A59X 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A59Y        TCGA-KK-A59Z        TCGA-KK-A5A1        TCGA-KK-A6DY 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A6E0        TCGA-KK-A6E1        TCGA-KK-A6E2        TCGA-KK-A6E4 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A6E5        TCGA-KK-A6E6        TCGA-KK-A6E7        TCGA-KK-A6E8 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A7AP        TCGA-KK-A7AQ        TCGA-KK-A7AU        TCGA-KK-A7AV 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A7AW        TCGA-KK-A7AY        TCGA-KK-A7AZ        TCGA-KK-A7B0 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A7B1        TCGA-KK-A7B2        TCGA-KK-A7B3        TCGA-KK-A7B4 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A8I4        TCGA-KK-A8I5        TCGA-KK-A8I6        TCGA-KK-A8I7 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A8I8        TCGA-KK-A8I9        TCGA-KK-A8IA        TCGA-KK-A8IB 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A8IC        TCGA-KK-A8ID        TCGA-KK-A8IF        TCGA-KK-A8IG 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A8IH        TCGA-KK-A8II        TCGA-KK-A8IJ        TCGA-KK-A8IK 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-KK-A8IL        TCGA-KK-A8IM        TCGA-M7-A71Y        TCGA-M7-A71Z 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-M7-A720        TCGA-M7-A721        TCGA-M7-A722        TCGA-M7-A723 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-M7-A724        TCGA-M7-A725        TCGA-QU-A6IL        TCGA-QU-A6IM 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-QU-A6IN        TCGA-QU-A6IO        TCGA-QU-A6IP        TCGA-SU-A7E7 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-V1-A8MF        TCGA-V1-A8MG        TCGA-V1-A8MJ        TCGA-V1-A8MK 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-V1-A8ML        TCGA-V1-A8MM        TCGA-V1-A8MU        TCGA-V1-A8WL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-V1-A8WN        TCGA-V1-A8WS        TCGA-V1-A8WV        TCGA-V1-A8X3 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VN-A88I        TCGA-VN-A88K        TCGA-VN-A88L        TCGA-VN-A88M 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VN-A88N        TCGA-VN-A88O        TCGA-VN-A88P        TCGA-VN-A88Q 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VN-A88R        TCGA-VP-A872        TCGA-VP-A875        TCGA-VP-A876 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VP-A878        TCGA-VP-A879        TCGA-VP-A87B        TCGA-VP-A87C 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VP-A87D        TCGA-VP-A87E        TCGA-VP-A87H        TCGA-VP-A87J 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-VP-A87K        TCGA-WW-A8ZI        TCGA-X4-A8KQ        TCGA-X4-A8KS 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-XA-A8JR        TCGA-XJ-A83F        TCGA-XJ-A83H        TCGA-XJ-A9DI 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-XJ-A9DK        TCGA-XJ-A9DQ        TCGA-XJ-A9DX        TCGA-Y6-A8TL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YJ-A8SW        TCGA-YL-A8HJ        TCGA-YL-A8HK        TCGA-YL-A8HL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YL-A8HM        TCGA-YL-A8HO        TCGA-YL-A8S8        TCGA-YL-A8S9 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YL-A8SA        TCGA-YL-A8SB        TCGA-YL-A8SC        TCGA-YL-A8SF 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YL-A8SH        TCGA-YL-A8SJ        TCGA-YL-A8SK        TCGA-YL-A8SL 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YL-A8SO        TCGA-YL-A8SP        TCGA-YL-A8SQ        TCGA-YL-A8SR 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-YL-A9WH        TCGA-YL-A9WI        TCGA-YL-A9WJ        TCGA-YL-A9WK 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-ZG-A8QW        TCGA-ZG-A8QX        TCGA-ZG-A8QY        TCGA-ZG-A8QZ 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
D60V7, continuous
D60V8, continuous
D60V9, continuous
D60V10, continuous
D60V11, continuous
D60V12, continuous
D60V13, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PRTFDC1 MUTATED       0                         0     2
  PRTFDC1 WILD-TYPE     2                         7   145
D60V14, multiclass
[1] "Remove cluster labels:" "PRTFDC1 MUTATED"       
clus
  PRTFDC1 MUTATED PRTFDC1 WILD-TYPE 
                2               154 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5745 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5746        TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5752        TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5762        TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5766        TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5771        TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-CH-5790        TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5494        TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5498        TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5503 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7321        TCGA-EJ-7327 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7793        TCGA-EJ-7794        TCGA-EJ-7797 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-FC-7708        TCGA-FC-7961        TCGA-G9-6329        TCGA-G9-6332 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338        TCGA-G9-6342 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351        TCGA-G9-6353 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362        TCGA-G9-6363 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366        TCGA-G9-6367 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371        TCGA-G9-6373 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384        TCGA-G9-6385 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499        TCGA-H9-7775 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7075        TCGA-HC-7077        TCGA-HC-7078        TCGA-HC-7079 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7080        TCGA-HC-7081        TCGA-HC-7209        TCGA-HC-7210 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7211        TCGA-HC-7212        TCGA-HC-7213        TCGA-HC-7230 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7231        TCGA-HC-7232        TCGA-HC-7233        TCGA-HC-7737 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7738        TCGA-HC-7740        TCGA-HC-7742        TCGA-HC-7744 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7745        TCGA-HC-7747        TCGA-HC-7748        TCGA-HC-7749 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7750        TCGA-HC-7752        TCGA-HC-7818        TCGA-HC-7819 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HC-7820        TCGA-HC-7821        TCGA-HI-7168        TCGA-HI-7169 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 
       TCGA-HI-7170        TCGA-HI-7171 
"PRTFDC1 WILD-TYPE" "PRTFDC1 WILD-TYPE" 

Clustering(61) Variable = PCSK5 MUTATION ANALYSIS
D61V1, survival
                 sevent
clus2               0   1
  PCSK5 MUTATED     6   0
  PCSK5 WILD-TYPE 406   7
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              6             413 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
              0               7 
$`PCSK5 MUTATED`
TCGA-CH-5748 TCGA-FC-7961 TCGA-FC-A4JI TCGA-G9-6378 TCGA-G9-6384 TCGA-KK-A59V 
        1.02        15.42        13.45        37.97        25.15       113.10 

$`PCSK5 WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5750 TCGA-CH-5751 
       13.97         1.97         2.99        24.03        13.02        35.01 
TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
       31.00         1.02         2.04         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 
        1.02        23.01         1.02        15.06        24.03         2.04 
TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 
       13.02        15.98        26.99         9.99        32.02        33.01 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        29.00        27.16        33.11        19.56        13.32 
TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 
       29.79        46.52        44.88        26.30        45.73        28.93 
TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       30.31        27.19        23.90        38.93        48.13        36.69 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       48.53        38.53        36.23        60.23        46.55        47.80 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 
       52.27        64.50        51.88        68.35        43.07        36.66 
TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 
       38.76        39.75        60.23        41.85        47.87        29.06 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 TCGA-EJ-7314 
       88.34        74.10        93.70        83.57        36.13        37.81 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7325 TCGA-EJ-7327 
       33.14        25.35        33.83        27.09        35.18        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-A5OB TCGA-FC-A66V TCGA-FC-A6HD TCGA-FC-A8O0 
        4.54        28.41        22.36        17.23        16.24         1.78 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6339 
       41.62        87.35        81.04        67.99        66.67        83.87 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 
       55.76        18.21        68.68        49.81        46.16        50.70 
TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
       49.35        47.15        46.52        47.44        45.30        39.39 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       44.81         3.32        40.18        39.95        38.01        40.31 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6379 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       26.66        31.50        58.45        27.29        58.22        56.75 
TCGA-G9-6498 TCGA-G9-6499 TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 
       64.18        50.73        38.96        27.91        30.97        35.34 
TCGA-G9-7523 TCGA-G9-7525 TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 
       28.18        32.68         6.08        30.94         3.68        19.76 
TCGA-HC-7078 TCGA-HC-7079 TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 
       65.26         2.93        36.36        37.35        14.47        28.54 
TCGA-HC-7211 TCGA-HC-7212 TCGA-HC-7213 TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 
        0.79        28.60        40.08         1.68         2.37        38.17 
TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 
       44.55         0.72         2.10        31.69        23.57         1.48 
TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 
        1.68        23.70        24.59        26.04         1.97        17.16 
TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 
       25.71        30.51        30.84        17.85        24.56        31.43 
TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 
       19.36        22.42        28.27        23.87         2.17         2.27 
TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 
       22.55        17.95        22.32         1.58        15.88         1.15 
TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN 
       22.36         0.76         1.78         2.01         2.20         1.61 
TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY 
       17.42         2.33         3.48         1.45         1.25         4.41 
TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 
        7.00         4.93         9.53        25.48        18.84        78.61 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K 
       88.24        82.92        43.69        20.19        12.30        33.01 
TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R 
       25.32        30.94        16.54        27.58        32.05        29.92 
TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I 
       27.39         6.02        25.28        27.91        16.83        22.52 
TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B 
       22.88        10.78        23.67        14.37        20.28        13.87 
TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN 
        5.85         6.97        10.62        13.32        15.22        40.67 
TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN TCGA-KC-A4BO TCGA-KC-A4BR TCGA-KC-A4BV 
       12.69        30.71        59.67        19.96        44.35        43.66 
TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA TCGA-KC-A7FD TCGA-KC-A7FE 
       21.86         2.99         8.65        19.66         8.88        11.57 
TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 TCGA-KK-A6DY TCGA-KK-A6E0 
       56.28        44.68        86.40        77.72       115.86        30.02 
TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 TCGA-KK-A6E5 TCGA-KK-A6E6 
       54.54       165.17        67.59       115.13        49.25       113.33 
TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ TCGA-KK-A7AU TCGA-KK-A7AV 
       67.07        58.19         6.44        52.93        58.36        27.02 
TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 TCGA-KK-A7B1 TCGA-KK-A7B2 
       34.65        51.68        49.94        32.84        34.95        36.13 
TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 TCGA-KK-A8I6 TCGA-KK-A8I7 
       29.56        20.94        67.99       101.79        21.96        65.82 
TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB TCGA-KK-A8IC TCGA-KK-A8ID 
       31.79        32.91        63.48         2.73        67.43        69.27 
TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II TCGA-KK-A8IJ TCGA-KK-A8IK 
       26.43        82.36        66.18       113.98        51.25        51.39 
TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z TCGA-M7-A720 TCGA-M7-A721 
       20.65        47.28         5.19        21.14        12.62        13.15 
TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 TCGA-QU-A6IL TCGA-QU-A6IM 
       34.85        25.08        29.23        18.84         3.19        41.00 
TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 TCGA-V1-A8MF TCGA-V1-A8MG 
      140.19       122.17        86.14        18.12        41.23        28.18 
TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM TCGA-V1-A8MU TCGA-V1-A8WL 
       40.44        16.70        14.73        39.29        53.16        52.08 
TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 TCGA-VN-A88I TCGA-VN-A88K 
       30.38        15.58        22.55         6.64         8.84        25.51 
TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O TCGA-VN-A88P TCGA-VN-A88Q 
       24.53         6.21        15.52        15.81        41.42        44.91 
TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 TCGA-VP-A878 TCGA-VP-A879 
       25.78       111.39        75.91       109.58        97.41        23.93 
TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E TCGA-VP-A87H TCGA-VP-A87J 
       85.18        55.56        60.92        66.97        21.80        53.36 
TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS TCGA-XA-A8JR TCGA-XJ-A83F 
       42.94        14.76        45.47        32.19         3.91        37.05 
TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK TCGA-XJ-A9DQ TCGA-XJ-A9DX 
       38.04        42.08        48.03         9.04         2.99        31.99 
TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK TCGA-YL-A8HL TCGA-YL-A8HM 
       25.48         4.87        52.96        49.02        51.45        48.72 
TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA TCGA-YL-A8SB TCGA-YL-A8SC 
       71.77        62.14        60.56        16.83        56.52        41.46 
TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK TCGA-YL-A8SL TCGA-YL-A8SO 
       45.14        28.77        45.86        46.29        32.45       114.38 
TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH TCGA-YL-A9WI TCGA-YL-A9WJ 
       71.34        62.79         8.98        14.04        53.36        60.99 
TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY TCGA-ZG-A8QZ 
       62.37         3.09        14.53        13.28        10.13 

  PCSK5 MUTATED PCSK5 WILD-TYPE 
           1.02            0.72 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         113.10          165.17 
  PCSK5 MUTATED PCSK5 WILD-TYPE 
         20.285          27.390 
[1] "1.0 - 113.1 (20.3)" "0.7 - 165.2 (27.4)"
[1] "hr="     "9100000"
D61V2, continuous
                 vv
clus               T2  T3  T4
  PCSK5 MUTATED     1   5   0
  PCSK5 WILD-TYPE 171 234   6
D61V3, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  T2             1             171
  T3             5             234
  T4             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"
D61V4, binary
                 cls
clus                0   1
  PCSK5 MUTATED     4   0
  PCSK5 WILD-TYPE 295  58
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      4    0
  PCSK5 WILD-TYPE  295   58
   clus
vv  PCSK5 MUTATED PCSK5 WILD-TYPE
  0             4             295
  1             0              58
[1] 2 2
[1] FALSE
D61V5, binary
                 cls
clus                0   1
  PCSK5 MUTATED     0   6
  PCSK5 WILD-TYPE  15 399
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCSK5 MUTATED      0    6
  PCSK5 WILD-TYPE   15  399
                                        clus
vv                                       PCSK5 MUTATED PCSK5 WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE             0              15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                6             399
[1] 2 2
[1] FALSE
                 vv
clus               R0  R1  R2  RX
  PCSK5 MUTATED     3   2   0   0
  PCSK5 WILD-TYPE 280 101   5  15
D61V6, multiclass
    clus
vv   PCSK5 MUTATED PCSK5 WILD-TYPE
  R0             3             280
  R1             2             101
  R2             0               5
  RX             0              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, continuous
D61V8, continuous
D61V9, continuous
D61V10, continuous
D61V11, continuous
D61V12, continuous
D61V13, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCSK5 MUTATED       0                         1     3
  PCSK5 WILD-TYPE     2                         6   144
D61V14, multiclass
                           clus
vv                          PCSK5 MUTATED PCSK5 WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             1               6
  WHITE                                 3             144
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = ITGA2B MUTATION ANALYSIS
D62V1, survival
                  sevent
clus2                0   1
  ITGA2B MUTATED     4   0
  ITGA2B WILD-TYPE 408   7
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               4              415 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               0                7 
$`ITGA2B MUTATED`
TCGA-EJ-7325 TCGA-HC-7212 TCGA-KC-A4BR TCGA-KK-A59V 
       35.18        28.60        44.35       113.10 

$`ITGA2B WILD-TYPE`
TCGA-2A-A8VL TCGA-2A-A8VO TCGA-2A-A8VT TCGA-2A-A8VV TCGA-2A-A8VX TCGA-2A-A8W1 
       20.42        43.79        32.71        22.06        33.96         3.68 
TCGA-2A-A8W3 TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 
       25.35         2.99         6.97        22.06         1.02        12.99 
TCGA-CH-5743 TCGA-CH-5744 TCGA-CH-5745 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 
       13.97         1.97         2.99        24.03         1.02        13.02 
TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 
       35.01        31.00         1.02         2.04         0.92        44.02 
TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 
       12.00         1.02        23.01         1.02        15.06        24.03 
TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 
        2.04        13.02        15.98        26.99         9.99        32.02 
TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 
       33.01         2.99        29.00        27.16        33.11        19.56 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.32        29.79        46.52        44.88        26.30        45.73 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 
       28.93        30.31        27.19        23.90        38.93        48.13 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.69        48.53        38.53        36.23        60.23        46.55 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       47.80        52.27        64.50        51.88        68.35        43.07 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       36.66        38.76        39.75        60.23        41.85        47.87 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7218 TCGA-EJ-7312 
       29.06        88.34        74.10        93.70        83.57        36.13 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7318 TCGA-EJ-7321 TCGA-EJ-7327 
       37.81        33.14        25.35        33.83        27.09        30.35 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
       27.68         6.28        24.39        23.90        38.37        25.87 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
       25.68        20.55        14.53        14.14        18.15        19.59 
TCGA-EJ-7792 TCGA-EJ-7793 TCGA-EJ-7794 TCGA-EJ-7797 TCGA-EJ-8468 TCGA-EJ-8469 
       17.29         3.75        23.05        19.92        77.16        76.41 
TCGA-EJ-8470 TCGA-EJ-8472 TCGA-EJ-8474 TCGA-EJ-A46B TCGA-EJ-A46D TCGA-EJ-A46E 
       38.10        24.85        25.18        21.60        20.58        17.23 
TCGA-EJ-A46F TCGA-EJ-A46G TCGA-EJ-A46H TCGA-EJ-A46I TCGA-EJ-A65B TCGA-EJ-A65D 
       25.74        21.96        23.80        21.96        23.34        12.92 
TCGA-EJ-A65E TCGA-EJ-A65F TCGA-EJ-A65G TCGA-EJ-A65J TCGA-EJ-A65M TCGA-EJ-A6RA 
       13.71        18.41        21.90        14.83         7.56        11.61 
TCGA-EJ-A6RC TCGA-EJ-A7NF TCGA-EJ-A7NG TCGA-EJ-A7NH TCGA-EJ-A7NJ TCGA-EJ-A7NK 
       28.70         8.22        14.20        15.58         6.48        15.65 
TCGA-EJ-A7NM TCGA-EJ-A7NN TCGA-EJ-A8FN TCGA-EJ-A8FO TCGA-EJ-A8FP TCGA-EJ-A8FS 
        4.21         6.48        10.82         9.27         9.83         8.75 
TCGA-EJ-A8FU TCGA-FC-7708 TCGA-FC-7961 TCGA-FC-A4JI TCGA-FC-A5OB TCGA-FC-A66V 
        4.54        28.41        15.42        13.45        22.36        17.23 
TCGA-FC-A6HD TCGA-FC-A8O0 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 
       16.24         1.78        41.62        87.35        81.04        67.99 
TCGA-G9-6338 TCGA-G9-6339 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6347 TCGA-G9-6348 
       66.67        83.87        55.76        18.21        68.68        49.81 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6354 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       46.16        50.70        49.35        47.15        46.52        47.44 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       45.30        39.39        44.81         3.32        40.18        39.95 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6379 
       38.01        40.31        26.66        31.50        37.97        58.45 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6498 TCGA-G9-6499 
       25.15        27.29        58.22        56.75        64.18        50.73 
TCGA-G9-7510 TCGA-G9-7519 TCGA-G9-7521 TCGA-G9-7522 TCGA-G9-7523 TCGA-G9-7525 
       38.96        27.91        30.97        35.34        28.18        32.68 
TCGA-H9-7775 TCGA-H9-A6BX TCGA-H9-A6BY TCGA-HC-7075 TCGA-HC-7078 TCGA-HC-7079 
        6.08        30.94         3.68        19.76        65.26         2.93 
TCGA-HC-7080 TCGA-HC-7081 TCGA-HC-7209 TCGA-HC-7210 TCGA-HC-7211 TCGA-HC-7213 
       36.36        37.35        14.47        28.54         0.79        40.08 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HC-7232 TCGA-HC-7233 TCGA-HC-7736 TCGA-HC-7737 
        1.68         2.37        38.17        44.55         0.72         2.10 
TCGA-HC-7738 TCGA-HC-7740 TCGA-HC-7742 TCGA-HC-7744 TCGA-HC-7745 TCGA-HC-7747 
       31.69        23.57         1.48         1.68        23.70        24.59 
TCGA-HC-7748 TCGA-HC-7749 TCGA-HC-7750 TCGA-HC-7752 TCGA-HC-7817 TCGA-HC-7818 
       26.04         1.97        17.16        25.71        30.51        30.84 
TCGA-HC-7819 TCGA-HC-7820 TCGA-HC-7821 TCGA-HC-8213 TCGA-HC-8216 TCGA-HC-8256 
       17.85        24.56        31.43        19.36        22.42        28.27 
TCGA-HC-8257 TCGA-HC-8258 TCGA-HC-8259 TCGA-HC-8260 TCGA-HC-8261 TCGA-HC-8262 
       23.87         2.17         2.27        22.55        17.95        22.32 
TCGA-HC-8264 TCGA-HC-8265 TCGA-HC-8266 TCGA-HC-A48F TCGA-HC-A4ZV TCGA-HC-A631 
        1.58        15.88         1.15        22.36         0.76         1.78 
TCGA-HC-A632 TCGA-HC-A6AL TCGA-HC-A6AN TCGA-HC-A6AO TCGA-HC-A6AP TCGA-HC-A6AQ 
        2.01         2.20         1.61        17.42         2.33         3.48 
TCGA-HC-A6AS TCGA-HC-A6HX TCGA-HC-A6HY TCGA-HC-A76W TCGA-HC-A76X TCGA-HC-A8CY 
        1.45         1.25         4.41         7.00         4.93         9.53 
TCGA-HC-A8D0 TCGA-HC-A8D1 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       25.48        18.84        78.61        88.24        82.92        43.69 
TCGA-J4-8198 TCGA-J4-8200 TCGA-J4-A67K TCGA-J4-A67L TCGA-J4-A67M TCGA-J4-A67N 
       20.19        12.30        33.01        25.32        30.94        16.54 
TCGA-J4-A67O TCGA-J4-A67Q TCGA-J4-A67R TCGA-J4-A67S TCGA-J4-A67T TCGA-J4-A6G1 
       27.58        32.05        29.92        27.39         6.02        25.28 
TCGA-J4-A6G3 TCGA-J4-A6M7 TCGA-J4-A83I TCGA-J4-A83J TCGA-J4-A83K TCGA-J4-A83L 
       27.91        16.83        22.52        22.88        10.78        23.67 
TCGA-J4-A83M TCGA-J4-A83N TCGA-J9-A52B TCGA-J9-A52C TCGA-J9-A52D TCGA-J9-A52E 
       14.37        20.28        13.87         5.85         6.97        10.62 
TCGA-J9-A8CL TCGA-J9-A8CM TCGA-J9-A8CN TCGA-J9-A8CP TCGA-KC-A4BL TCGA-KC-A4BN 
       13.32        15.22        40.67        12.69        30.71        59.67 
TCGA-KC-A4BO TCGA-KC-A4BV TCGA-KC-A7F3 TCGA-KC-A7F5 TCGA-KC-A7F6 TCGA-KC-A7FA 
       19.96        43.66        21.86         2.99         8.65        19.66 
TCGA-KC-A7FD TCGA-KC-A7FE TCGA-KK-A59X TCGA-KK-A59Y TCGA-KK-A59Z TCGA-KK-A5A1 
        8.88        11.57        56.28        44.68        86.40        77.72 
TCGA-KK-A6DY TCGA-KK-A6E0 TCGA-KK-A6E1 TCGA-KK-A6E2 TCGA-KK-A6E3 TCGA-KK-A6E4 
      115.86        30.02        54.54       165.17        67.59       115.13 
TCGA-KK-A6E5 TCGA-KK-A6E6 TCGA-KK-A6E7 TCGA-KK-A6E8 TCGA-KK-A7AP TCGA-KK-A7AQ 
       49.25       113.33        67.07        58.19         6.44        52.93 
TCGA-KK-A7AU TCGA-KK-A7AV TCGA-KK-A7AW TCGA-KK-A7AY TCGA-KK-A7AZ TCGA-KK-A7B0 
       58.36        27.02        34.65        51.68        49.94        32.84 
TCGA-KK-A7B1 TCGA-KK-A7B2 TCGA-KK-A7B3 TCGA-KK-A7B4 TCGA-KK-A8I4 TCGA-KK-A8I5 
       34.95        36.13        29.56        20.94        67.99       101.79 
TCGA-KK-A8I6 TCGA-KK-A8I7 TCGA-KK-A8I8 TCGA-KK-A8I9 TCGA-KK-A8IA TCGA-KK-A8IB 
       21.96        65.82        31.79        32.91        63.48         2.73 
TCGA-KK-A8IC TCGA-KK-A8ID TCGA-KK-A8IF TCGA-KK-A8IG TCGA-KK-A8IH TCGA-KK-A8II 
       67.43        69.27        26.43        82.36        66.18       113.98 
TCGA-KK-A8IJ TCGA-KK-A8IK TCGA-KK-A8IL TCGA-KK-A8IM TCGA-M7-A71Y TCGA-M7-A71Z 
       51.25        51.39        20.65        47.28         5.19        21.14 
TCGA-M7-A720 TCGA-M7-A721 TCGA-M7-A722 TCGA-M7-A723 TCGA-M7-A724 TCGA-M7-A725 
       12.62        13.15        34.85        25.08        29.23        18.84 
TCGA-QU-A6IL TCGA-QU-A6IM TCGA-QU-A6IN TCGA-QU-A6IO TCGA-QU-A6IP TCGA-SU-A7E7 
        3.19        41.00       140.19       122.17        86.14        18.12 
TCGA-V1-A8MF TCGA-V1-A8MG TCGA-V1-A8MJ TCGA-V1-A8MK TCGA-V1-A8ML TCGA-V1-A8MM 
       41.23        28.18        40.44        16.70        14.73        39.29 
TCGA-V1-A8MU TCGA-V1-A8WL TCGA-V1-A8WN TCGA-V1-A8WS TCGA-V1-A8WV TCGA-V1-A8X3 
       53.16        52.08        30.38        15.58        22.55         6.64 
TCGA-VN-A88I TCGA-VN-A88K TCGA-VN-A88L TCGA-VN-A88M TCGA-VN-A88N TCGA-VN-A88O 
        8.84        25.51        24.53         6.21        15.52        15.81 
TCGA-VN-A88P TCGA-VN-A88Q TCGA-VN-A88R TCGA-VP-A872 TCGA-VP-A875 TCGA-VP-A876 
       41.42        44.91        25.78       111.39        75.91       109.58 
TCGA-VP-A878 TCGA-VP-A879 TCGA-VP-A87B TCGA-VP-A87C TCGA-VP-A87D TCGA-VP-A87E 
       97.41        23.93        85.18        55.56        60.92        66.97 
TCGA-VP-A87H TCGA-VP-A87J TCGA-VP-A87K TCGA-WW-A8ZI TCGA-X4-A8KQ TCGA-X4-A8KS 
       21.80        53.36        42.94        14.76        45.47        32.19 
TCGA-XA-A8JR TCGA-XJ-A83F TCGA-XJ-A83G TCGA-XJ-A83H TCGA-XJ-A9DI TCGA-XJ-A9DK 
        3.91        37.05        38.04        42.08        48.03         9.04 
TCGA-XJ-A9DQ TCGA-XJ-A9DX TCGA-Y6-A8TL TCGA-YJ-A8SW TCGA-YL-A8HJ TCGA-YL-A8HK 
        2.99        31.99        25.48         4.87        52.96        49.02 
TCGA-YL-A8HL TCGA-YL-A8HM TCGA-YL-A8HO TCGA-YL-A8S8 TCGA-YL-A8S9 TCGA-YL-A8SA 
       51.45        48.72        71.77        62.14        60.56        16.83 
TCGA-YL-A8SB TCGA-YL-A8SC TCGA-YL-A8SF TCGA-YL-A8SH TCGA-YL-A8SJ TCGA-YL-A8SK 
       56.52        41.46        45.14        28.77        45.86        46.29 
TCGA-YL-A8SL TCGA-YL-A8SO TCGA-YL-A8SP TCGA-YL-A8SQ TCGA-YL-A8SR TCGA-YL-A9WH 
       32.45       114.38        71.34        62.79         8.98        14.04 
TCGA-YL-A9WI TCGA-YL-A9WJ TCGA-YL-A9WK TCGA-ZG-A8QW TCGA-ZG-A8QX TCGA-ZG-A8QY 
       53.36        60.99        62.37         3.09        14.53        13.28 
TCGA-ZG-A8QZ 
       10.13 

  ITGA2B MUTATED ITGA2B WILD-TYPE 
           28.60             0.72 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
          113.10           165.17 
  ITGA2B MUTATED ITGA2B WILD-TYPE 
          39.765           27.160 
[1] "28.6 - 113.1 (39.8)" "0.7 - 165.2 (27.2)" 
[1] "hr="     "9100000"
D62V2, continuous
                  vv
clus                T2  T3  T4
  ITGA2B MUTATED     1   3   0
  ITGA2B WILD-TYPE 171 236   6
D62V3, multiclass
    clus
vv   ITGA2B MUTATED ITGA2B WILD-TYPE
  T2              1              171
  T3              3              236
  T4              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"
D62V4, binary
                  cls
clus                 0   1
  ITGA2B MUTATED     3   1
  ITGA2B WILD-TYPE 296  57
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED      3    1
  ITGA2B WILD-TYPE  296   57
   clus
vv  ITGA2B MUTATED ITGA2B WILD-TYPE
  0              3              296
  1              1               57
[1] 2 2
[1] FALSE
D62V5, binary
                  cls
clus                 0   1
  ITGA2B MUTATED     0   4
  ITGA2B WILD-TYPE  15 401
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ITGA2B MUTATED      0    4
  ITGA2B WILD-TYPE   15  401
                                        clus
vv                                       ITGA2B MUTATED ITGA2B WILD-TYPE
  PROSTATE ADENOCARCINOMA  OTHER SUBTYPE              0               15
  PROSTATE ADENOCARCINOMA ACINAR TYPE                 4              401
[1] 2 2
[1] FALSE
                  vv
clus                R0  R1  R2  RX
  ITGA2B MUTATED     3   0   0   0
  ITGA2B WILD-TYPE 280 103   5  15
D62V6, multiclass
    clus
vv   ITGA2B MUTATED ITGA2B WILD-TYPE
  R0              3              280
  R1              0              103
  R2              0                5
  RX              0               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, continuous
D62V8, continuous
D62V9, continuous
D62V10, continuous
D62V11, continuous
D62V12, continuous
D62V13, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ITGA2B MUTATED       0                         0     1
  ITGA2B WILD-TYPE     2                         7   146
D62V14, multiclass
[1] "Remove cluster labels:" "ITGA2B MUTATED"        
clus
  ITGA2B MUTATED ITGA2B WILD-TYPE 
               1              155 
      TCGA-CH-5737       TCGA-CH-5738       TCGA-CH-5739       TCGA-CH-5740 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5741       TCGA-CH-5743       TCGA-CH-5744       TCGA-CH-5745 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5746       TCGA-CH-5748       TCGA-CH-5750       TCGA-CH-5751 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5752       TCGA-CH-5753       TCGA-CH-5754       TCGA-CH-5761 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5762       TCGA-CH-5763       TCGA-CH-5764       TCGA-CH-5765 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5766       TCGA-CH-5767       TCGA-CH-5768       TCGA-CH-5769 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5771       TCGA-CH-5772       TCGA-CH-5788       TCGA-CH-5789 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-CH-5790       TCGA-CH-5791       TCGA-CH-5792       TCGA-CH-5794 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5494       TCGA-EJ-5495       TCGA-EJ-5496       TCGA-EJ-5497 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5498       TCGA-EJ-5499       TCGA-EJ-5501       TCGA-EJ-5503 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5504       TCGA-EJ-5505       TCGA-EJ-5506       TCGA-EJ-5507 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5508       TCGA-EJ-5509       TCGA-EJ-5510       TCGA-EJ-5511 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5512       TCGA-EJ-5514       TCGA-EJ-5515       TCGA-EJ-5516 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5517       TCGA-EJ-5518       TCGA-EJ-5519       TCGA-EJ-5521 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5522       TCGA-EJ-5524       TCGA-EJ-5525       TCGA-EJ-5526 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5527       TCGA-EJ-5530       TCGA-EJ-5531       TCGA-EJ-5532 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-5542       TCGA-EJ-7115       TCGA-EJ-7123       TCGA-EJ-7125 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7314       TCGA-EJ-7315       TCGA-EJ-7317       TCGA-EJ-7321 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7327       TCGA-EJ-7328       TCGA-EJ-7330       TCGA-EJ-7331 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7781       TCGA-EJ-7782       TCGA-EJ-7783       TCGA-EJ-7784 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7785       TCGA-EJ-7786       TCGA-EJ-7788       TCGA-EJ-7789 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7791       TCGA-EJ-7792       TCGA-EJ-7793       TCGA-EJ-7794 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-EJ-7797       TCGA-FC-7708       TCGA-FC-7961       TCGA-G9-6329 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6332       TCGA-G9-6333       TCGA-G9-6336       TCGA-G9-6338 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6342       TCGA-G9-6343       TCGA-G9-6348       TCGA-G9-6351 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6353       TCGA-G9-6356       TCGA-G9-6361       TCGA-G9-6362 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6363       TCGA-G9-6364       TCGA-G9-6365       TCGA-G9-6366 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6367       TCGA-G9-6369       TCGA-G9-6370       TCGA-G9-6371 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6373       TCGA-G9-6377       TCGA-G9-6378       TCGA-G9-6384 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-G9-6385       TCGA-G9-6494       TCGA-G9-6496       TCGA-G9-6499 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-H9-7775       TCGA-HC-7075       TCGA-HC-7077       TCGA-HC-7078 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7079       TCGA-HC-7080       TCGA-HC-7081       TCGA-HC-7209 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7210       TCGA-HC-7211       TCGA-HC-7213       TCGA-HC-7230 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7231       TCGA-HC-7232       TCGA-HC-7233       TCGA-HC-7736 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7737       TCGA-HC-7738       TCGA-HC-7740       TCGA-HC-7742 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7744       TCGA-HC-7745       TCGA-HC-7747       TCGA-HC-7748 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7749       TCGA-HC-7750       TCGA-HC-7752       TCGA-HC-7818 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HC-7819       TCGA-HC-7820       TCGA-HC-7821       TCGA-HI-7168 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
      TCGA-HI-7169       TCGA-HI-7170       TCGA-HI-7171 
"ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" "ITGA2B WILD-TYPE" 
